POP-OUT | CLOSE

An Information Portal to 111558 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4GBU
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8.3
    Temperature 277.0
    Details 35% Peg400, 0.2M MgCl2, 0.1M Na Hepes, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 141.12 α = 90
    b = 141.12 β = 90
    c = 42.81 γ = 90
     
    Space Group
    Space Group Name:    P 43 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 270
    Collection Date 2011-08-15
     
    Diffraction Radiation
    Monochromator Si (111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X6A
    Wavelength List 0.9795
    Site NSLS
    Beamline X6A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.0
    Observed Criterion Sigma(I) 1.0
    Resolution(High) 1.18
    Resolution(Low) 24
    Number Reflections(Observed) 999641
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.076
    Redundancy 7.1
     
    High Resolution Shell Details
    Resolution(High) 1.18
    Resolution(Low) 1.22
    Percent Possible(All) 99.7
    R Merge I(Observed) 0.554
    Mean I Over Sigma(Observed) 2.04
    R-Sym I(Observed) 0.554
    Redundancy 6.6
    Number Unique Reflections(All) 13937
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.179
    Resolution(Low) 21.037
    Cut-off Sigma(F) 1.35
    Number of Reflections(Observed) 141257
    Number of Reflections(R-Free) 14125
    Percent Reflections(Observed) 99.71
    R-Factor(Observed) 0.102
    R-Work 0.0999
    R-Free 0.121
    R-Free Selection Details random 10%
     
    Temperature Factor Modeling
    Data Not Available
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.1795
    Shell Resolution(Low) 1.1929
    Number of Reflections(R-Free) 463
    Number of Reflections(R-Work) 4168
    R-Factor(R-Work) 0.1708
    R-Factor(R-Free) 0.2012
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.1929
    Shell Resolution(Low) 1.2069
    Number of Reflections(R-Free) 460
    Number of Reflections(R-Work) 4146
    R-Factor(R-Work) 0.1523
    R-Factor(R-Free) 0.1943
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2069
    Shell Resolution(Low) 1.2216
    Number of Reflections(R-Free) 470
    Number of Reflections(R-Work) 4221
    R-Factor(R-Work) 0.1421
    R-Factor(R-Free) 0.1719
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2216
    Shell Resolution(Low) 1.2371
    Number of Reflections(R-Free) 461
    Number of Reflections(R-Work) 4144
    R-Factor(R-Work) 0.1382
    R-Factor(R-Free) 0.1666
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2371
    Shell Resolution(Low) 1.2534
    Number of Reflections(R-Free) 467
    Number of Reflections(R-Work) 4215
    R-Factor(R-Work) 0.1358
    R-Factor(R-Free) 0.1674
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2534
    Shell Resolution(Low) 1.2705
    Number of Reflections(R-Free) 469
    Number of Reflections(R-Work) 4217
    R-Factor(R-Work) 0.137
    R-Factor(R-Free) 0.1608
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2705
    Shell Resolution(Low) 1.2887
    Number of Reflections(R-Free) 464
    Number of Reflections(R-Work) 4170
    R-Factor(R-Work) 0.1303
    R-Factor(R-Free) 0.1542
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2887
    Shell Resolution(Low) 1.3079
    Number of Reflections(R-Free) 469
    Number of Reflections(R-Work) 4223
    R-Factor(R-Work) 0.1199
    R-Factor(R-Free) 0.1612
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3079
    Shell Resolution(Low) 1.3284
    Number of Reflections(R-Free) 468
    Number of Reflections(R-Work) 4210
    R-Factor(R-Work) 0.1101
    R-Factor(R-Free) 0.1482
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3284
    Shell Resolution(Low) 1.3501
    Number of Reflections(R-Free) 466
    Number of Reflections(R-Work) 4204
    R-Factor(R-Work) 0.1017
    R-Factor(R-Free) 0.1352
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3501
    Shell Resolution(Low) 1.3734
    Number of Reflections(R-Free) 470
    Number of Reflections(R-Work) 4222
    R-Factor(R-Work) 0.0929
    R-Factor(R-Free) 0.1278
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3734
    Shell Resolution(Low) 1.3984
    Number of Reflections(R-Free) 467
    Number of Reflections(R-Work) 4195
    R-Factor(R-Work) 0.0907
    R-Factor(R-Free) 0.1205
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3984
    Shell Resolution(Low) 1.4253
    Number of Reflections(R-Free) 471
    Number of Reflections(R-Work) 4243
    R-Factor(R-Work) 0.0879
    R-Factor(R-Free) 0.1276
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4253
    Shell Resolution(Low) 1.4544
    Number of Reflections(R-Free) 466
    Number of Reflections(R-Work) 4196
    R-Factor(R-Work) 0.0861
    R-Factor(R-Free) 0.1199
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4544
    Shell Resolution(Low) 1.486
    Number of Reflections(R-Free) 470
    Number of Reflections(R-Work) 4231
    R-Factor(R-Work) 0.0887
    R-Factor(R-Free) 0.1179
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.486
    Shell Resolution(Low) 1.5205
    Number of Reflections(R-Free) 471
    Number of Reflections(R-Work) 4242
    R-Factor(R-Work) 0.0768
    R-Factor(R-Free) 0.1078
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5205
    Shell Resolution(Low) 1.5585
    Number of Reflections(R-Free) 466
    Number of Reflections(R-Work) 4192
    R-Factor(R-Work) 0.0662
    R-Factor(R-Free) 0.1039
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5585
    Shell Resolution(Low) 1.6007
    Number of Reflections(R-Free) 473
    Number of Reflections(R-Work) 4257
    R-Factor(R-Work) 0.0662
    R-Factor(R-Free) 0.0977
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6007
    Shell Resolution(Low) 1.6478
    Number of Reflections(R-Free) 473
    Number of Reflections(R-Work) 4256
    R-Factor(R-Work) 0.0635
    R-Factor(R-Free) 0.091
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6478
    Shell Resolution(Low) 1.7009
    Number of Reflections(R-Free) 471
    Number of Reflections(R-Work) 4236
    R-Factor(R-Work) 0.0676
    R-Factor(R-Free) 0.0931
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7009
    Shell Resolution(Low) 1.7617
    Number of Reflections(R-Free) 469
    Number of Reflections(R-Work) 4228
    R-Factor(R-Work) 0.0702
    R-Factor(R-Free) 0.0944
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7617
    Shell Resolution(Low) 1.8322
    Number of Reflections(R-Free) 473
    Number of Reflections(R-Work) 4256
    R-Factor(R-Work) 0.0744
    R-Factor(R-Free) 0.0989
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8322
    Shell Resolution(Low) 1.9155
    Number of Reflections(R-Free) 475
    Number of Reflections(R-Work) 4268
    R-Factor(R-Work) 0.0771
    R-Factor(R-Free) 0.11
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9155
    Shell Resolution(Low) 2.0164
    Number of Reflections(R-Free) 473
    Number of Reflections(R-Work) 4264
    R-Factor(R-Work) 0.0806
    R-Factor(R-Free) 0.1075
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0164
    Shell Resolution(Low) 2.1426
    Number of Reflections(R-Free) 475
    Number of Reflections(R-Work) 4288
    R-Factor(R-Work) 0.0835
    R-Factor(R-Free) 0.0982
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1426
    Shell Resolution(Low) 2.3079
    Number of Reflections(R-Free) 474
    Number of Reflections(R-Work) 4260
    R-Factor(R-Work) 0.0828
    R-Factor(R-Free) 0.1022
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3079
    Shell Resolution(Low) 2.5398
    Number of Reflections(R-Free) 477
    Number of Reflections(R-Work) 4300
    R-Factor(R-Work) 0.092
    R-Factor(R-Free) 0.1117
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5398
    Shell Resolution(Low) 2.9065
    Number of Reflections(R-Free) 477
    Number of Reflections(R-Work) 4290
    R-Factor(R-Work) 0.1064
    R-Factor(R-Free) 0.1216
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9065
    Shell Resolution(Low) 3.6587
    Number of Reflections(R-Free) 483
    Number of Reflections(R-Work) 4346
    R-Factor(R-Work) 0.12
    R-Factor(R-Free) 0.1271
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6587
    Shell Resolution(Low) 21.0404
    Number of Reflections(R-Free) 494
    Number of Reflections(R-Work) 4444
    R-Factor(R-Work) 0.1382
    R-Factor(R-Free) 0.14
    Percent Reflections(Observed) 97.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.01
    f_chiral_restr 0.132
    f_dihedral_angle_d 17.478
    f_angle_d 1.475
    f_bond_d 0.01
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3167
    Nucleic Acid Atoms 0
    Heterogen Atoms 107
    Solvent Atoms 658
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CBASS
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.8_1069)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.8_1069)
    model building PHASER
    data collection CBASS