메뉴 건너뛰기




Volumn 275, Issue 1, 2008, Pages 1-21

Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures

Author keywords

Protein crystallography; Protein Data Bank; R factor; Resolution; Restraints; Structure determination; Structure interpretation; Structure quality; Structure refinement; Structure validation

Indexed keywords

HYDROGEN; METAL ION; NUCLEIC ACID; PROTEIN; RANPIRNASE; SOLVENT;

EID: 37349016530     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2007.06178.x     Document Type: Review
Times cited : (219)

References (81)
  • 4
    • 33847616971 scopus 로고    scopus 로고
    • Growth of novel protein structural data
    • Levitt M (2007) Growth of novel protein structural data. Proc Natl Acad Sci USA 104, 3183 3188.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 3183-3188
    • Levitt, M.1
  • 6
    • 37349040500 scopus 로고    scopus 로고
    • Structure quality: Crystal structures in 'hotter' journals tend to have more errors
    • Borman S (2007) Structure quality: crystal structures in 'hotter' journals tend to have more errors. Chem Eng News 85, 11.
    • (2007) Chem Eng News , vol.85 , pp. 11
    • Borman, S.1
  • 7
    • 0022333121 scopus 로고
    • Stereochemically restrained refinement of macromolecular structures
    • Hendrickson WA (1985) Stereochemically restrained refinement of macromolecular structures. Methods Enzymol 115, 252 270.
    • (1985) Methods Enzymol , vol.115 , pp. 252-270
    • Hendrickson, W.A.1
  • 8
    • 0029644940 scopus 로고
    • Where freedom is given, liberties are taken
    • Kleywegt GJ Jones TA (1995) Where freedom is given, liberties are taken. Structure 3, 535 540.
    • (1995) Structure , vol.3 , pp. 535-540
    • Kleywegt, G.J.1    Jones, T.A.2
  • 9
    • 79952608525 scopus 로고
    • Accurate bond and angle parameters for X-ray protein-structure refinement
    • Engh R Huber R (1991) Accurate bond and angle parameters for X-ray protein-structure refinement. Acta Crystallogr D Biol Crystallogr 47, 392 400.
    • (1991) Acta Crystallogr D Biol Crystallogr , vol.47 , pp. 392-400
    • Engh, R.1    Huber, R.2
  • 10
    • 0141880996 scopus 로고    scopus 로고
    • Structure quality and target parameters
    • In. vol. F (. Rossman, M.G. Arnold, E., eds), pp. Kluwer, Dordrecht.
    • Engh RA Huber R (2001) Structure quality and target parameters. In International Tables for Crystallography vol. F (Rossman MG Arnold E, eds), pp. 382 392. Kluwer, Dordrecht.
    • (2001) International Tables for Crystallography , pp. 382-392
    • Engh, R.A.1    Huber, R.2
  • 11
    • 0001752768 scopus 로고    scopus 로고
    • The Cambridge Structural Database: A quarter of a million crystal structures and rising
    • Allen FH (2002) The Cambridge Structural Database: a quarter of a million crystal structures and rising. Acta Crystallogr D Biol Crystallogr 58, 380 388.
    • (2002) Acta Crystallogr D Biol Crystallogr , vol.58 , pp. 380-388
    • Allen, F.H.1
  • 12
    • 34247534257 scopus 로고    scopus 로고
    • Stereochemical restraints revisited: How accurate are refinement targets and how much should protein structures be allowed to deviate from them?
    • Jaskolski M, Gilski M, Dauter Z Wlodawer A (2007) Stereochemical restraints revisited: how accurate are refinement targets and how much should protein structures be allowed to deviate from them? Acta Crystallogr D Biol Crystallogr 63, 611 620.
    • (2007) Acta Crystallogr D Biol Crystallogr , vol.63 , pp. 611-620
    • Jaskolski, M.1    Gilski, M.2    Dauter, Z.3    Wlodawer, A.4
  • 13
    • 33646260450 scopus 로고    scopus 로고
    • Optimal description of a protein structure in terms of multiple groups undergoing TLS motion
    • Painter J Merritt EA (2006) Optimal description of a protein structure in terms of multiple groups undergoing TLS motion. Acta Crystallogr D Biol Crystallogr 62, 439 450.
    • (2006) Acta Crystallogr D Biol Crystallogr , vol.62 , pp. 439-450
    • Painter, J.1    Merritt, E.A.2
  • 14
    • 0001644632 scopus 로고
    • Between objectivity and subjectivity
    • Brändén C-I Jones TA (1990) Between objectivity and subjectivity. Nature 343, 687 689.
    • (1990) Nature , vol.343 , pp. 687-689
    • Brändén, C.-I.1    Jones, T.A.2
  • 19
    • 0014432781 scopus 로고
    • Solvent content of protein crystals
    • Matthews BW (1968) Solvent content of protein crystals. J Mol Biol 33, 491 497.
    • (1968) J Mol Biol , vol.33 , pp. 491-497
    • Matthews, B.W.1
  • 22
  • 23
    • 33748644877 scopus 로고    scopus 로고
    • Structure of a bacterial multidrug ABC transporter
    • Dawson RJ Locher KP (2006) Structure of a bacterial multidrug ABC transporter. Nature 443, 180 185.
    • (2006) Nature , vol.443 , pp. 180-185
    • Dawson, R.J.1    Locher, K.P.2
  • 24
    • 0033607003 scopus 로고    scopus 로고
    • Placement of protein and RNA structures into a 5 Å resolution map of the 50S ribosomal subunit
    • Ban N, Nissen P, Hansen J, Capel M, Moore PB Steitz TA (1999) Placement of protein and RNA structures into a 5 Å resolution map of the 50S ribosomal subunit. Nature 400, 841 847.
    • (1999) Nature , vol.400 , pp. 841-847
    • Ban, N.1    Nissen, P.2    Hansen, J.3    Capel, M.4    Moore, P.B.5    Steitz, T.A.6
  • 25
    • 0034637111 scopus 로고    scopus 로고
    • The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution
    • Ban N, Nissen P, Hansen J, Moore PB Steitz TA (2000) The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289, 905 920.
    • (2000) Science , vol.289 , pp. 905-920
    • Ban, N.1    Nissen, P.2    Hansen, J.3    Moore, P.B.4    Steitz, T.A.5
  • 28
    • 84943920736 scopus 로고
    • Phase annealing in SHELX-90: Direct methods for larger structures
    • Sheldrick GM (1990) Phase annealing in SHELX-90: direct methods for larger structures. Acta Crystallogr D Biol Crystallogr 46, 467 473.
    • (1990) Acta Crystallogr D Biol Crystallogr , vol.46 , pp. 467-473
    • Sheldrick, G.M.1
  • 32
    • 0030915704 scopus 로고    scopus 로고
    • Improved R-factors for diffraction data analysis in macromolecular crystallography
    • Diederichs K Karplus PA (1997) Improved R-factors for diffraction data analysis in macromolecular crystallography. Nat Struct Biol 4, 269 275.
    • (1997) Nat Struct Biol , vol.4 , pp. 269-275
    • Diederichs, K.1    Karplus, P.A.2
  • 33
    • 0000330205 scopus 로고    scopus 로고
    • On the use of the merging R factor as a quality indicator for X-ray data
    • Weiss MS Hilgenfeld R (1997) On the use of the merging R factor as a quality indicator for X-ray data. J Appl Crystallogr 30, 203 205.
    • (1997) J Appl Crystallogr , vol.30 , pp. 203-205
    • Weiss, M.S.1    Hilgenfeld, R.2
  • 34
    • 0141987861 scopus 로고    scopus 로고
    • 'Cool' crystals: Macromolecular cryocrystallography and radiation damage
    • Garman E (2003) 'Cool' crystals: macromolecular cryocrystallography and radiation damage. Curr Opin Struct Biol 13, 545 551.
    • (2003) Curr Opin Struct Biol , vol.13 , pp. 545-551
    • Garman, E.1
  • 35
    • 33749179561 scopus 로고    scopus 로고
    • Radiation damage in macromolecular cryocrystallography
    • Ravelli RB Garman EF (2006) Radiation damage in macromolecular cryocrystallography. Curr Opin Struct Biol 16, 624 629.
    • (2006) Curr Opin Struct Biol , vol.16 , pp. 624-629
    • Ravelli, R.B.1    Garman, E.F.2
  • 38
    • 0039299578 scopus 로고    scopus 로고
    • Who checks the checkers? Four validation tools applied to eight atomic resolution structures
    • EU 3-D Validation Network (
    • EU 3-D Validation Network (1998) Who checks the checkers? Four validation tools applied to eight atomic resolution structures. J Mol Biol 276, 417 436.
    • (1998) J Mol Biol , vol.276 , pp. 417-436
  • 39
    • 4444330868 scopus 로고    scopus 로고
    • Crystal structure of a novel antifungal protein distinct with five disulfide bridges from Eucommia ulmoides Oliver at an atomic resolution
    • Xiang Y, Huang RH, Liu XZ, Zhang Y Wang DC (2004) Crystal structure of a novel antifungal protein distinct with five disulfide bridges from Eucommia ulmoides Oliver at an atomic resolution. J Struct Biol 148, 86 97.
    • (2004) J Struct Biol , vol.148 , pp. 86-97
    • Xiang, Y.1    Huang, R.H.2    Liu, X.Z.3    Zhang, Y.4    Wang, D.C.5
  • 41
    • 0026597444 scopus 로고
    • The free R value: A novel statistical quantity for assessing the accuracy of crystal structures
    • Brünger AT (1992) The free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355, 472 474.
    • (1992) Nature , vol.355 , pp. 472-474
    • Brünger, A.T.1
  • 42
    • 34548319255 scopus 로고    scopus 로고
    • Separating model optimization and model validation in statistical cross-validation as applied to crystallography
    • Kleywegt GJ (2007) Separating model optimization and model validation in statistical cross-validation as applied to crystallography. Acta Crystallogr D Biol Crystallogr 63, 939 940.
    • (2007) Acta Crystallogr D Biol Crystallogr , vol.63 , pp. 939-940
    • Kleywegt, G.J.1
  • 43
    • 0012220002 scopus 로고
    • Tests for statistical significance
    • In: vol. IV. Ibers, J.A. Hamilton, W.C., eds), pp. The Kynoch Press, Birmingham.
    • Hamilton W (1974) Tests for statistical significance. In : International Tables for X-ray Crystallography, vol. IV Ibers JA Hamilton WC, eds), pp. 285 292. The Kynoch Press, Birmingham.
    • (1974) International Tables for X-ray Crystallography , pp. 285-292
    • Hamilton, W.1
  • 45
    • 3242886389 scopus 로고    scopus 로고
    • Molprobity: Structure validation and all-atom contact analysis for nucleic acids and their complexes
    • Davis IW, Murray LW, Richardson JS Richardson DC (2004) molprobity: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res 32, W615 W619.
    • (2004) Nucleic Acids Res , vol.32
    • Davis, I.W.1    Murray, L.W.2    Richardson, J.S.3    Richardson, D.C.4
  • 46
    • 0013815214 scopus 로고
    • Stereochemical criteria for polypeptide and protein chain conformations. II Allowed conformation for a pair of peptide units
    • Ramakrishnan C Ramachandran GN (1965) Stereochemical criteria for polypeptide and protein chain conformations. II Allowed conformation for a pair of peptide units. Biophys J 5, 909 933.
    • (1965) Biophys J , vol.5 , pp. 909-933
    • Ramakrishnan, C.1    Ramachandran, G.N.2
  • 50
    • 34547763220 scopus 로고    scopus 로고
    • Crystallography: Crystallographic evidence for deviating C3b structure
    • Janssen BJ, Read RJ, Brünger AT Gros P (2007) Crystallography: crystallographic evidence for deviating C3b structure. Nature 448, E1 E2.
    • (2007) Nature , vol.448
    • Janssen, B.J.1    Read, R.J.2    Brünger, A.T.3    Gros, P.4
  • 52
    • 0037880292 scopus 로고
    • Reexamination of the three-dimensional structure of the small subunit of RuBisCo from higher plants
    • Knight S, Andersson I Brändén CI (1989) Reexamination of the three-dimensional structure of the small subunit of RuBisCo from higher plants. Science 244, 702 705.
    • (1989) Science , vol.244 , pp. 702-705
    • Knight, S.1    Andersson, I.2    Brändén, C.I.3
  • 54
    • 0035823075 scopus 로고    scopus 로고
    • Structure of MsbA from E. coli: A homolog of the multidrug resistance ATP binding cassette (ABC) transporters
    • Chang G Roth CB (2001) Structure of MsbA from E. coli: a homolog of the multidrug resistance ATP binding cassette (ABC) transporters. Science 293, 1793 1800.
    • (2001) Science , vol.293 , pp. 1793-1800
    • Chang, G.1    Roth, C.B.2
  • 56
    • 0024492495 scopus 로고
    • Crystal structure of a retroviral protease proves relationship to aspartic protease family
    • Miller M, Jaskólski M, Rao JKM, Leis J Wlodawer A (1989) Crystal structure of a retroviral protease proves relationship to aspartic protease family. Nature 337, 576 579.
    • (1989) Nature , vol.337 , pp. 576-579
    • Miller, M.1    Jaskólski, M.2    Rao, J.K.M.3    Leis, J.4    Wlodawer, A.5
  • 58
    • 0034669514 scopus 로고    scopus 로고
    • Structural basis for BABIM inhibition of botulinum neurotoxin type B protease
    • Hanson MA, Oost TK, Sukonpan C, Rich DH Stevens RC (2000) Structural basis for BABIM inhibition of botulinum neurotoxin type B protease. J Am Chem Soc 122, 11268 11269.
    • (2000) J Am Chem Soc , vol.122 , pp. 11268-11269
    • Hanson, M.A.1    Oost, T.K.2    Sukonpan, C.3    Rich, D.H.4    Stevens, R.C.5
  • 59
    • 0034881411 scopus 로고    scopus 로고
    • Questions about the structure of the botulinum neurotoxin B light chain in complex with a target peptide
    • Rupp B Segelke B (2001) Questions about the structure of the botulinum neurotoxin B light chain in complex with a target peptide. Nat Struct Biol 8, 663 664.
    • (2001) Nat Struct Biol , vol.8 , pp. 663-664
    • Rupp, B.1    Segelke, B.2
  • 60
    • 0033179802 scopus 로고    scopus 로고
    • The geometry of metal-ligand interactions relevant to proteins
    • Harding MM (1999) The geometry of metal-ligand interactions relevant to proteins. Acta Crystallogr D Biol Crystallogr 55, 1432 1443.
    • (1999) Acta Crystallogr D Biol Crystallogr , vol.55 , pp. 1432-1443
    • Harding, M.M.1
  • 61
    • 0036014793 scopus 로고    scopus 로고
    • Metal-ligand geometry relevant to proteins and in proteins: Sodium and potassium
    • Harding MM (2002) Metal-ligand geometry relevant to proteins and in proteins: sodium and potassium. Acta Crystallogr D Biol Crystallogr 58, 872 874.
    • (2002) Acta Crystallogr D Biol Crystallogr , vol.58 , pp. 872-874
    • Harding, M.M.1
  • 62
    • 33744502092 scopus 로고    scopus 로고
    • Small revisions to predicted distances around metal sites in proteins
    • Harding MM (2006) Small revisions to predicted distances around metal sites in proteins. Acta Crystallogr D Biol Crystallogr 62, 678 682.
    • (2006) Acta Crystallogr D Biol Crystallogr , vol.62 , pp. 678-682
    • Harding, M.M.1
  • 64
    • 84872498969 scopus 로고
    • Chemical and steric constraints in inorganic solids
    • Brown ID (1992) Chemical and steric constraints in inorganic solids. Acta Crystallogr D Biol Crystallogr 48, 553 572.
    • (1992) Acta Crystallogr D Biol Crystallogr , vol.48 , pp. 553-572
    • Brown, I.D.1
  • 65
  • 66
    • 0000046122 scopus 로고
    • Location of hydrogen atoms in certain heterocyclic compounds
    • Singh C (1965) Location of hydrogen atoms in certain heterocyclic compounds. Acta Crystallogr D Biol Crystallogr 19, 861 864.
    • (1965) Acta Crystallogr D Biol Crystallogr , vol.19 , pp. 861-864
    • Singh, C.1
  • 67
    • 0020388106 scopus 로고
    • Neutron diffraction of crystalline proteins
    • Wlodawer A (1982) Neutron diffraction of crystalline proteins. Prog Biophys Mol Biol 40, 115 159.
    • (1982) Prog Biophys Mol Biol , vol.40 , pp. 115-159
    • Wlodawer, A.1
  • 68
    • 32044434962 scopus 로고    scopus 로고
    • Recent results on hydrogen and hydration in biology studied by neutron macromolecular crystallography
    • Niimura N, Arai S, Kurihara K, Chatake T, Tanaka I Bau R (2006) Recent results on hydrogen and hydration in biology studied by neutron macromolecular crystallography. Cell Mol Life Sci 63, 285 300.
    • (2006) Cell Mol Life Sci , vol.63 , pp. 285-300
    • Niimura, N.1    Arai, S.2    Kurihara, K.3    Chatake, T.4    Tanaka, I.5    Bau, R.6
  • 70
    • 0028584269 scopus 로고
    • Crystal structure of the catalytic domain of HIV-1 integrase: Similarity to other polynucleotidyl transferases
    • Dyda F, Hickman AB, Jenkins TM, Engelman A, Craigie R Davies DR (1994) Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transferases. Science 266, 1981 1986.
    • (1994) Science , vol.266 , pp. 1981-1986
    • Dyda, F.1    Hickman, A.B.2    Jenkins, T.M.3    Engelman, A.4    Craigie, R.5    Davies, D.R.6
  • 72
    • 0029643858 scopus 로고    scopus 로고
    • The catalytic domain of avian sarcoma virus integrase: Conformation of the active-site residues in the presence of divalent cations
    • Bujacz G, Jaskólski M, Alexandratos J, Wlodawer A, Merkel G, Katz RA Skalka AM (1996) The catalytic domain of avian sarcoma virus integrase: conformation of the active-site residues in the presence of divalent cations. Structure 4, 89 96.
    • (1996) Structure , vol.4 , pp. 89-96
    • Bujacz, G.1    Jaskólski, M.2    Alexandratos, J.3    Wlodawer, A.4    Merkel, G.5    Katz, R.A.6    Skalka, A.M.7
  • 73
    • 0032544311 scopus 로고    scopus 로고
    • Crystal structures of the catalytic domain of HIV-1 integrase free and complexed with its metal cofactor: High level of similarity of the active site with other viral integrases
    • Maignan S, Guilloteau JP, Zhou-Liu Q, Clement-Mella C Mikol V (1998) Crystal structures of the catalytic domain of HIV-1 integrase free and complexed with its metal cofactor: high level of similarity of the active site with other viral integrases. J Mol Biol 282, 359 368.
    • (1998) J Mol Biol , vol.282 , pp. 359-368
    • Maignan, S.1    Guilloteau, J.P.2    Zhou-Liu, Q.3    Clement-Mella, C.4    Mikol, V.5
  • 76
    • 11144230028 scopus 로고    scopus 로고
    • The active site of a Lon protease from Methanococcus jannaschii distinctly differs from the canonical catalytic dyad of Lon proteases
    • Im YJ, Na Y, Kang GB, Rho SH, Kim MK, Lee JH, Chung CH Eom SH (2004) The active site of a Lon protease from Methanococcus jannaschii distinctly differs from the canonical catalytic dyad of Lon proteases. J Biol Chem 279, 53451 53457.
    • (2004) J Biol Chem , vol.279 , pp. 53451-53457
    • Im, Y.J.1    Na, Y.2    Kang, G.B.3    Rho, S.H.4    Kim, M.K.5    Lee, J.H.6    Chung, C.H.7    Eom, S.H.8
  • 77
    • 22044455121 scopus 로고    scopus 로고
    • Atomic-resolution crystal structure of the proteolytic domain of Archaeoglobus fulgidus Lon reveals the conformational variability in the active sites of Lon proteases
    • Botos I, Melnikov EE, Cherry S, Kozlov S, Makhovskaya OV, Tropea JE, Gustchina A, Rotanova TV Wlodawer A (2005) Atomic-resolution crystal structure of the proteolytic domain of Archaeoglobus fulgidus Lon reveals the conformational variability in the active sites of Lon proteases. J Mol Biol 351, 144 157.
    • (2005) J Mol Biol , vol.351 , pp. 144-157
    • Botos, I.1    Melnikov, E.E.2    Cherry, S.3    Kozlov, S.4    Makhovskaya, O.V.5    Tropea, J.E.6    Gustchina, A.7    Rotanova, T.V.8    Wlodawer, A.9
  • 78
    • 1242274650 scopus 로고    scopus 로고
    • Automated protein crystal structure determination using elves
    • Holton J Alber T (2004) Automated protein crystal structure determination using elves. Proc Natl Acad Sci USA 101, 1537 1542.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 1537-1542
    • Holton, J.1    Alber, T.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.