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X-RAY DIFFRACTION
Materials and Methods page
4IFD
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 6.5
    Temperature 292.0
    Details 0.02M Tris pH7.5, 0.05M NaCl, 0.001M MnCl2, 0.002M MgCl2, 1mM TCEP, 0.15M MES pH6.5, 0.27M NaBr, 11.4-12.2% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 292K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 154.09 α = 90
    b = 107.44 β = 110.63
    c = 150.46 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector PIXEL
    Type PSI PILATUS 6M
    Collection Date 2011-10-28
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SLS BEAMLINE X10SA
    Wavelength List 0.9199
    Site SLS
    Beamline X10SA
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.81
    Resolution(Low) 49.64
    Number Reflections(All) 99137
    Number Reflections(Observed) 99137
    Percent Possible(Observed) 87.4
    R Merge I(Observed) 0.176
    B(Isotropic) From Wilson Plot 59.5
    Redundancy 12.8
     
    High Resolution Shell Details
    Resolution(High) 2.8
    Resolution(Low) 3.0
    Percent Possible(All) 56.5
    R Merge I(Observed) 0.548
    Mean I Over Sigma(Observed) 1.89
    Redundancy 2.5
    Number Unique Reflections(All) 11922
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.805
    Resolution(Low) 49.638
    Cut-off Sigma(F) 1.99
    Number of Reflections(all) 99137
    Number of Reflections(Observed) 99101
    Number of Reflections(R-Free) 4956
    Percent Reflections(Observed) 87.86
    R-Factor(All) 0.1846
    R-Factor(Observed) 0.1846
    R-Work 0.1825
    R-Free 0.2239
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Data Not Available
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8046
    Shell Resolution(Low) 2.8365
    Number of Reflections(Observed) 1336
    Number of Reflections(R-Free) 70
    Number of Reflections(R-Work) 1336
    R-Factor(R-Work) 0.3046
    R-Factor(R-Free) 0.3492
    Percent Reflections(Observed) 38.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8365
    Shell Resolution(Low) 2.8698
    Number of Reflections(Observed) 2015
    Number of Reflections(R-Free) 106
    Number of Reflections(R-Work) 2015
    R-Factor(R-Work) 0.2932
    R-Factor(R-Free) 0.3581
    Percent Reflections(Observed) 57.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8698
    Shell Resolution(Low) 2.9048
    Number of Reflections(Observed) 2312
    Number of Reflections(R-Free) 122
    Number of Reflections(R-Work) 2312
    R-Factor(R-Work) 0.2938
    R-Factor(R-Free) 0.3046
    Percent Reflections(Observed) 64.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9048
    Shell Resolution(Low) 2.9416
    Number of Reflections(Observed) 2233
    Number of Reflections(R-Free) 117
    Number of Reflections(R-Work) 2233
    R-Factor(R-Work) 0.2924
    R-Factor(R-Free) 0.3456
    Percent Reflections(Observed) 64.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9416
    Shell Resolution(Low) 2.9803
    Number of Reflections(Observed) 2316
    Number of Reflections(R-Free) 122
    Number of Reflections(R-Work) 2316
    R-Factor(R-Work) 0.2869
    R-Factor(R-Free) 0.3634
    Percent Reflections(Observed) 64.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9803
    Shell Resolution(Low) 3.0211
    Number of Reflections(Observed) 2217
    Number of Reflections(R-Free) 117
    Number of Reflections(R-Work) 2217
    R-Factor(R-Work) 0.2787
    R-Factor(R-Free) 0.3229
    Percent Reflections(Observed) 63.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0211
    Shell Resolution(Low) 3.0643
    Number of Reflections(Observed) 2287
    Number of Reflections(R-Free) 120
    Number of Reflections(R-Work) 2287
    R-Factor(R-Work) 0.2636
    R-Factor(R-Free) 0.3362
    Percent Reflections(Observed) 64.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0643
    Shell Resolution(Low) 3.11
    Number of Reflections(Observed) 2256
    Number of Reflections(R-Free) 119
    Number of Reflections(R-Work) 2256
    R-Factor(R-Work) 0.2602
    R-Factor(R-Free) 0.3132
    Percent Reflections(Observed) 64.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.11
    Shell Resolution(Low) 3.1586
    Number of Reflections(Observed) 2516
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2516
    R-Factor(R-Work) 0.2539
    R-Factor(R-Free) 0.2924
    Percent Reflections(Observed) 71.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1586
    Shell Resolution(Low) 3.2104
    Number of Reflections(Observed) 3109
    Number of Reflections(R-Free) 163
    Number of Reflections(R-Work) 3109
    R-Factor(R-Work) 0.2524
    R-Factor(R-Free) 0.3102
    Percent Reflections(Observed) 87.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2104
    Shell Resolution(Low) 3.2657
    Number of Reflections(Observed) 3510
    Number of Reflections(R-Free) 185
    Number of Reflections(R-Work) 3510
    R-Factor(R-Work) 0.2401
    R-Factor(R-Free) 0.293
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2657
    Shell Resolution(Low) 3.3251
    Number of Reflections(Observed) 3532
    Number of Reflections(R-Free) 186
    Number of Reflections(R-Work) 3532
    R-Factor(R-Work) 0.233
    R-Factor(R-Free) 0.309
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3251
    Shell Resolution(Low) 3.389
    Number of Reflections(Observed) 3541
    Number of Reflections(R-Free) 186
    Number of Reflections(R-Work) 3541
    R-Factor(R-Work) 0.219
    R-Factor(R-Free) 0.2526
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.389
    Shell Resolution(Low) 3.4582
    Number of Reflections(Observed) 3589
    Number of Reflections(R-Free) 189
    Number of Reflections(R-Work) 3589
    R-Factor(R-Work) 0.2142
    R-Factor(R-Free) 0.2614
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4582
    Shell Resolution(Low) 3.5334
    Number of Reflections(Observed) 3544
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 3544
    R-Factor(R-Work) 0.1959
    R-Factor(R-Free) 0.2645
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5334
    Shell Resolution(Low) 3.6155
    Number of Reflections(Observed) 3574
    Number of Reflections(R-Free) 188
    Number of Reflections(R-Work) 3574
    R-Factor(R-Work) 0.1948
    R-Factor(R-Free) 0.2249
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6155
    Shell Resolution(Low) 3.7059
    Number of Reflections(Observed) 3567
    Number of Reflections(R-Free) 188
    Number of Reflections(R-Work) 3567
    R-Factor(R-Work) 0.1853
    R-Factor(R-Free) 0.2292
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7059
    Shell Resolution(Low) 3.8061
    Number of Reflections(Observed) 3539
    Number of Reflections(R-Free) 186
    Number of Reflections(R-Work) 3539
    R-Factor(R-Work) 0.176
    R-Factor(R-Free) 0.2475
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8061
    Shell Resolution(Low) 3.918
    Number of Reflections(Observed) 3585
    Number of Reflections(R-Free) 189
    Number of Reflections(R-Work) 3585
    R-Factor(R-Work) 0.17
    R-Factor(R-Free) 0.2031
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.918
    Shell Resolution(Low) 4.0445
    Number of Reflections(Observed) 3557
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 3557
    R-Factor(R-Work) 0.1698
    R-Factor(R-Free) 0.1905
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0445
    Shell Resolution(Low) 4.1889
    Number of Reflections(Observed) 3589
    Number of Reflections(R-Free) 189
    Number of Reflections(R-Work) 3589
    R-Factor(R-Work) 0.1593
    R-Factor(R-Free) 0.2161
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1889
    Shell Resolution(Low) 4.3566
    Number of Reflections(Observed) 3570
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 3570
    R-Factor(R-Work) 0.1505
    R-Factor(R-Free) 0.1891
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3566
    Shell Resolution(Low) 4.5547
    Number of Reflections(Observed) 3568
    Number of Reflections(R-Free) 188
    Number of Reflections(R-Work) 3568
    R-Factor(R-Work) 0.1432
    R-Factor(R-Free) 0.1786
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5547
    Shell Resolution(Low) 4.7947
    Number of Reflections(Observed) 3576
    Number of Reflections(R-Free) 188
    Number of Reflections(R-Work) 3576
    R-Factor(R-Work) 0.1365
    R-Factor(R-Free) 0.1722
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7947
    Shell Resolution(Low) 5.0948
    Number of Reflections(Observed) 3612
    Number of Reflections(R-Free) 191
    Number of Reflections(R-Work) 3612
    R-Factor(R-Work) 0.1433
    R-Factor(R-Free) 0.176
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0948
    Shell Resolution(Low) 5.4877
    Number of Reflections(Observed) 3561
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 3561
    R-Factor(R-Work) 0.1577
    R-Factor(R-Free) 0.2146
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.4877
    Shell Resolution(Low) 6.0391
    Number of Reflections(Observed) 3600
    Number of Reflections(R-Free) 190
    Number of Reflections(R-Work) 3600
    R-Factor(R-Work) 0.1712
    R-Factor(R-Free) 0.2358
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.0391
    Shell Resolution(Low) 6.9109
    Number of Reflections(Observed) 3610
    Number of Reflections(R-Free) 190
    Number of Reflections(R-Work) 3610
    R-Factor(R-Work) 0.1814
    R-Factor(R-Free) 0.2234
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.9109
    Shell Resolution(Low) 8.6994
    Number of Reflections(Observed) 3623
    Number of Reflections(R-Free) 190
    Number of Reflections(R-Work) 3623
    R-Factor(R-Work) 0.1584
    R-Factor(R-Free) 0.1779
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.6994
    Shell Resolution(Low) 49.6458
    Number of Reflections(Observed) 3701
    Number of Reflections(R-Free) 196
    Number of Reflections(R-Work) 3701
    R-Factor(R-Work) 0.159
    R-Factor(R-Free) 0.175
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.035
    f_dihedral_angle_d 9.903
    f_angle_d 0.542
    f_bond_d 0.003
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 25991
    Nucleic Acid Atoms 540
    Heterogen Atoms 54
    Solvent Atoms 244
     
     
  •   Software and Computing Hide
    Computing
    Data Collection RemDAQ
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.8.1_1168)
    model building PHASER
    data collection RemDAQ