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X-RAY DIFFRACTION
Materials and Methods page
4H83
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    Temperature 294.0
    Details 0.1 M Sodium Citrate, 20% (w/v) PEG 4000, 5% (v/v) 2-Propanol, VAPOR DIFFUSION, SITTING DROP, temperature 294K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 89.98 α = 90
    b = 102.95 β = 90
    c = 234.43 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Collection Date 2012-04-27
     
    Diffraction Radiation
    Monochromator Double silicon(111) crystal
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X29A
    Wavelength List 1.075
    Site NSLS
    Beamline X29A
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.1
    Resolution(Low) 50
    Number Reflections(Observed) 113134
    Percent Possible(Observed) 87.9
    R Merge I(Observed) 0.091
    B(Isotropic) From Wilson Plot 23.77
    Redundancy 10.5
     
    High Resolution Shell Details
    Resolution(High) 2.1
    Resolution(Low) 2.14
    Percent Possible(All) 78.8
    R Merge I(Observed) 0.92
    Mean I Over Sigma(Observed) 2.5
    Redundancy 10.5
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.094
    Resolution(Low) 47.131
    Cut-off Sigma(F) 1.34
    Number of Reflections(Observed) 107240
    Number of Reflections(R-Free) 5358
    Percent Reflections(Observed) 83.33
    R-Factor(Observed) 0.1501
    R-Work 0.1473
    R-Free 0.2044
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 28.849
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0937
    Shell Resolution(Low) 2.1175
    Number of Reflections(R-Free) 86
    Number of Reflections(R-Work) 1762
    R-Factor(R-Work) 0.1488
    R-Factor(R-Free) 0.2112
    Percent Reflections(Observed) 44.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1175
    Shell Resolution(Low) 2.1424
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 2118
    R-Factor(R-Work) 0.1472
    R-Factor(R-Free) 0.2382
    Percent Reflections(Observed) 52.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1424
    Shell Resolution(Low) 2.1685
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2408
    R-Factor(R-Work) 0.1523
    R-Factor(R-Free) 0.2131
    Percent Reflections(Observed) 60.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1685
    Shell Resolution(Low) 2.196
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2526
    R-Factor(R-Work) 0.1537
    R-Factor(R-Free) 0.2514
    Percent Reflections(Observed) 63.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.196
    Shell Resolution(Low) 2.2249
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2773
    R-Factor(R-Work) 0.1569
    R-Factor(R-Free) 0.262
    Percent Reflections(Observed) 69.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2249
    Shell Resolution(Low) 2.2553
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2817
    R-Factor(R-Work) 0.1544
    R-Factor(R-Free) 0.2179
    Percent Reflections(Observed) 70.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2553
    Shell Resolution(Low) 2.2876
    Number of Reflections(R-Free) 164
    Number of Reflections(R-Work) 2944
    R-Factor(R-Work) 0.1606
    R-Factor(R-Free) 0.2324
    Percent Reflections(Observed) 73.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2876
    Shell Resolution(Low) 2.3217
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 3029
    R-Factor(R-Work) 0.1532
    R-Factor(R-Free) 0.2351
    Percent Reflections(Observed) 74.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3217
    Shell Resolution(Low) 2.358
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 3092
    R-Factor(R-Work) 0.159
    R-Factor(R-Free) 0.2096
    Percent Reflections(Observed) 77.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.358
    Shell Resolution(Low) 2.3966
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 3182
    R-Factor(R-Work) 0.1574
    R-Factor(R-Free) 0.2454
    Percent Reflections(Observed) 79.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3966
    Shell Resolution(Low) 2.438
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 3220
    R-Factor(R-Work) 0.1499
    R-Factor(R-Free) 0.27
    Percent Reflections(Observed) 79.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.438
    Shell Resolution(Low) 2.4823
    Number of Reflections(R-Free) 177
    Number of Reflections(R-Work) 3211
    R-Factor(R-Work) 0.1478
    R-Factor(R-Free) 0.2309
    Percent Reflections(Observed) 80.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4823
    Shell Resolution(Low) 2.53
    Number of Reflections(R-Free) 174
    Number of Reflections(R-Work) 3258
    R-Factor(R-Work) 0.1574
    R-Factor(R-Free) 0.2176
    Percent Reflections(Observed) 81.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.53
    Shell Resolution(Low) 2.5817
    Number of Reflections(R-Free) 182
    Number of Reflections(R-Work) 3336
    R-Factor(R-Work) 0.1598
    R-Factor(R-Free) 0.1985
    Percent Reflections(Observed) 82.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5817
    Shell Resolution(Low) 2.6378
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 3400
    R-Factor(R-Work) 0.1611
    R-Factor(R-Free) 0.227
    Percent Reflections(Observed) 83.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6378
    Shell Resolution(Low) 2.6992
    Number of Reflections(R-Free) 201
    Number of Reflections(R-Work) 3378
    R-Factor(R-Work) 0.164
    R-Factor(R-Free) 0.2578
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6992
    Shell Resolution(Low) 2.7666
    Number of Reflections(R-Free) 169
    Number of Reflections(R-Work) 3518
    R-Factor(R-Work) 0.1633
    R-Factor(R-Free) 0.2273
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7666
    Shell Resolution(Low) 2.8414
    Number of Reflections(R-Free) 198
    Number of Reflections(R-Work) 3582
    R-Factor(R-Work) 0.1599
    R-Factor(R-Free) 0.23
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8414
    Shell Resolution(Low) 2.925
    Number of Reflections(R-Free) 181
    Number of Reflections(R-Work) 3735
    R-Factor(R-Work) 0.1575
    R-Factor(R-Free) 0.2249
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.925
    Shell Resolution(Low) 3.0194
    Number of Reflections(R-Free) 212
    Number of Reflections(R-Work) 3755
    R-Factor(R-Work) 0.1608
    R-Factor(R-Free) 0.2024
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0194
    Shell Resolution(Low) 3.1273
    Number of Reflections(R-Free) 215
    Number of Reflections(R-Work) 3909
    R-Factor(R-Work) 0.1587
    R-Factor(R-Free) 0.2307
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1273
    Shell Resolution(Low) 3.2525
    Number of Reflections(R-Free) 205
    Number of Reflections(R-Work) 3985
    R-Factor(R-Work) 0.1622
    R-Factor(R-Free) 0.1998
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2525
    Shell Resolution(Low) 3.4005
    Number of Reflections(R-Free) 206
    Number of Reflections(R-Work) 4013
    R-Factor(R-Work) 0.146
    R-Factor(R-Free) 0.1913
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4005
    Shell Resolution(Low) 3.5797
    Number of Reflections(R-Free) 226
    Number of Reflections(R-Work) 4010
    R-Factor(R-Work) 0.1461
    R-Factor(R-Free) 0.1886
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5797
    Shell Resolution(Low) 3.8039
    Number of Reflections(R-Free) 254
    Number of Reflections(R-Work) 4020
    R-Factor(R-Work) 0.1383
    R-Factor(R-Free) 0.1937
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8039
    Shell Resolution(Low) 4.0975
    Number of Reflections(R-Free) 198
    Number of Reflections(R-Work) 4088
    R-Factor(R-Work) 0.126
    R-Factor(R-Free) 0.1657
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0975
    Shell Resolution(Low) 4.5095
    Number of Reflections(R-Free) 180
    Number of Reflections(R-Work) 4146
    R-Factor(R-Work) 0.1156
    R-Factor(R-Free) 0.1644
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5095
    Shell Resolution(Low) 5.1614
    Number of Reflections(R-Free) 209
    Number of Reflections(R-Work) 4116
    R-Factor(R-Work) 0.1187
    R-Factor(R-Free) 0.1573
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1614
    Shell Resolution(Low) 6.5001
    Number of Reflections(R-Free) 207
    Number of Reflections(R-Work) 4205
    R-Factor(R-Work) 0.156
    R-Factor(R-Free) 0.21
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.5001
    Shell Resolution(Low) 47.1425
    Number of Reflections(R-Free) 238
    Number of Reflections(R-Work) 4346
    R-Factor(R-Work) 0.1625
    R-Factor(R-Free) 0.2095
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 14.208
    f_plane_restr 0.007
    f_chiral_restr 0.078
    f_angle_d 1.349
    f_bond_d 0.012
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 16810
    Nucleic Acid Atoms 0
    Heterogen Atoms 27
    Solvent Atoms 867
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CBASS
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) HKL-3000
    Structure Solution MOLREP
    Structure Refinement PHENIX (phenix.refine: 1.8_1069)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data collection DENZO