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X-RAY DIFFRACTION
Materials and Methods page
4H0D
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7.5
    Temperature 289.0
    Details 0.2 M sodium chloride, 0.1 M HEPES pH 7.5, 25 % w/v Polyethylene glycol 3,350, 10 mM manganese chloride, VAPOR DIFFUSION, SITTING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 39.1 α = 90
    b = 78.61 β = 90
    c = 133.71 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
    Details mirrors
    Collection Date 2011-10-09
     
    Diffraction Radiation
    Monochromator duoble crystal monochromator
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 19-ID
    Wavelength List 0.97924
    Site APS
    Beamline 19-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.5
    Resolution(Low) 50
    Number Reflections(All) 67113
    Number Reflections(Observed) 67113
    Percent Possible(Observed) 100.0
    B(Isotropic) From Wilson Plot 17.64
    Redundancy 7.8
     
    High Resolution Shell Details
    Resolution(High) 1.5
    Resolution(Low) 1.53
    Percent Possible(All) 100.0
    Mean I Over Sigma(Observed) 2.8
    R-Sym I(Observed) 0.664
    Redundancy 6.9
    Number Unique Reflections(All) 3259
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.498
    Resolution(Low) 38.771
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 67022
    Number of Reflections(Observed) 67022
    Number of Reflections(R-Free) 3398
    Percent Reflections(Observed) 99.64
    R-Factor(All) 0.122
    R-Factor(Observed) 0.122
    R-Work 0.12
    R-Free 0.158
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Isotropic Thermal Model anisotropic
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4978
    Shell Resolution(Low) 1.5192
    Number of Reflections(Observed) 2554
    Number of Reflections(R-Free) 113
    Number of Reflections(R-Work) 2441
    R-Factor(R-Work) 0.1442
    R-Factor(R-Free) 0.2414
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5192
    Shell Resolution(Low) 1.5419
    Number of Reflections(Observed) 2733
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2582
    R-Factor(R-Work) 0.133
    R-Factor(R-Free) 0.193
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5419
    Shell Resolution(Low) 1.566
    Number of Reflections(Observed) 2794
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2654
    R-Factor(R-Work) 0.1231
    R-Factor(R-Free) 0.2124
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.566
    Shell Resolution(Low) 1.5917
    Number of Reflections(Observed) 2710
    Number of Reflections(R-Free) 123
    Number of Reflections(R-Work) 2597
    R-Factor(R-Work) 0.1158
    R-Factor(R-Free) 0.1847
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5917
    Shell Resolution(Low) 1.6191
    Number of Reflections(Observed) 2785
    Number of Reflections(R-Free) 167
    Number of Reflections(R-Work) 2618
    R-Factor(R-Work) 0.1141
    R-Factor(R-Free) 0.1929
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6191
    Shell Resolution(Low) 1.6486
    Number of Reflections(Observed) 2756
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2619
    R-Factor(R-Work) 0.1099
    R-Factor(R-Free) 0.1975
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6486
    Shell Resolution(Low) 1.6803
    Number of Reflections(Observed) 2777
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2630
    R-Factor(R-Work) 0.1038
    R-Factor(R-Free) 0.1792
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6803
    Shell Resolution(Low) 1.7146
    Number of Reflections(Observed) 2759
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2629
    R-Factor(R-Work) 0.0987
    R-Factor(R-Free) 0.1629
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7146
    Shell Resolution(Low) 1.7519
    Number of Reflections(Observed) 2765
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2622
    R-Factor(R-Work) 0.1013
    R-Factor(R-Free) 0.1599
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7519
    Shell Resolution(Low) 1.7926
    Number of Reflections(Observed) 2793
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2639
    R-Factor(R-Work) 0.1053
    R-Factor(R-Free) 0.1692
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7926
    Shell Resolution(Low) 1.8375
    Number of Reflections(Observed) 2770
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2637
    R-Factor(R-Work) 0.0982
    R-Factor(R-Free) 0.1737
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8375
    Shell Resolution(Low) 1.8871
    Number of Reflections(Observed) 2780
    Number of Reflections(R-Free) 168
    Number of Reflections(R-Work) 2612
    R-Factor(R-Work) 0.0953
    R-Factor(R-Free) 0.1463
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8871
    Shell Resolution(Low) 1.9427
    Number of Reflections(Observed) 2788
    Number of Reflections(R-Free) 163
    Number of Reflections(R-Work) 2625
    R-Factor(R-Work) 0.0952
    R-Factor(R-Free) 0.1521
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9427
    Shell Resolution(Low) 2.0054
    Number of Reflections(Observed) 2773
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2636
    R-Factor(R-Work) 0.0958
    R-Factor(R-Free) 0.1381
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0054
    Shell Resolution(Low) 2.077
    Number of Reflections(Observed) 2805
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2662
    R-Factor(R-Work) 0.0961
    R-Factor(R-Free) 0.147
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.077
    Shell Resolution(Low) 2.1602
    Number of Reflections(Observed) 2797
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2654
    R-Factor(R-Work) 0.1002
    R-Factor(R-Free) 0.1504
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1602
    Shell Resolution(Low) 2.2585
    Number of Reflections(Observed) 2795
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2658
    R-Factor(R-Work) 0.1054
    R-Factor(R-Free) 0.1558
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2585
    Shell Resolution(Low) 2.3776
    Number of Reflections(Observed) 2801
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2650
    R-Factor(R-Work) 0.1102
    R-Factor(R-Free) 0.1583
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3776
    Shell Resolution(Low) 2.5265
    Number of Reflections(Observed) 2816
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2674
    R-Factor(R-Work) 0.1191
    R-Factor(R-Free) 0.1588
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5265
    Shell Resolution(Low) 2.7215
    Number of Reflections(Observed) 2830
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2683
    R-Factor(R-Work) 0.1251
    R-Factor(R-Free) 0.142
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7215
    Shell Resolution(Low) 2.9953
    Number of Reflections(Observed) 2848
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2715
    R-Factor(R-Work) 0.137
    R-Factor(R-Free) 0.157
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9953
    Shell Resolution(Low) 3.4285
    Number of Reflections(Observed) 2849
    Number of Reflections(R-Free) 126
    Number of Reflections(R-Work) 2723
    R-Factor(R-Work) 0.1339
    R-Factor(R-Free) 0.1626
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4285
    Shell Resolution(Low) 4.3186
    Number of Reflections(Observed) 2913
    Number of Reflections(R-Free) 118
    Number of Reflections(R-Work) 2795
    R-Factor(R-Work) 0.1233
    R-Factor(R-Free) 0.1613
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3186
    Shell Resolution(Low) 38.7845
    Number of Reflections(Observed) 3021
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2869
    R-Factor(R-Work) 0.1431
    R-Factor(R-Free) 0.1465
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.005
    f_chiral_restr 0.079
    f_dihedral_angle_d 14.527
    f_angle_d 1.132
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3586
    Nucleic Acid Atoms 0
    Heterogen Atoms 74
    Solvent Atoms 469
     
     
  •   Software and Computing Hide
    Computing
    Data Collection SBCCOLLECT, HKL3000
    Data Reduction (intensity integration) HKL-3000
    Data Reduction (data scaling) HKL-3000
    Structure Solution HKL3000, Molrep
    Structure Refinement PHENIX (phenix.refine: 1.8_1069)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.8_1069)
    model building Molrep
    model building HKL3000
    data collection HKL3000
    data collection SBCCOLLECT