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X-RAY DIFFRACTION
Materials and Methods page
3VCC
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8.5
    Temperature 293.0
    Details 25% PEG 3350, 0.1M Tris, 0.2M magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 154.35 α = 90
    b = 65.99 β = 93.56
    c = 75.64 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Collection Date 2010-10-29
     
    Diffraction Radiation
    Monochromator MIRRORS
    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
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.64
    Resolution(Low) 40.53
    Number Reflections(All) 84573
    Number Reflections(Observed) 84573
    Percent Possible(Observed) 90.93
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.64
    Resolution(Low) 40.525
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 84573
    Number of Reflections(Observed) 84573
    Number of Reflections(R-Free) 4220
    Percent Reflections(Observed) 90.93
    R-Factor(All) 0.1812
    R-Factor(Observed) 0.1812
    R-Work 0.1793
    R-Free 0.2164
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Anisotropic B[1][1] -0.4137
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -4.7336
    Anisotropic B[2][2] -1.2534
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 1.6671
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6397
    Shell Resolution(Low) 1.6583
    Number of Reflections(R-Free) 36
    Number of Reflections(R-Work) 754
    R-Factor(R-Work) 0.3879
    R-Factor(R-Free) 0.3775
    Percent Reflections(Observed) 26.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6583
    Shell Resolution(Low) 1.6778
    Number of Reflections(R-Free) 54
    Number of Reflections(R-Work) 1236
    R-Factor(R-Work) 0.3626
    R-Factor(R-Free) 0.3534
    Percent Reflections(Observed) 42.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6778
    Shell Resolution(Low) 1.6983
    Number of Reflections(R-Free) 81
    Number of Reflections(R-Work) 1512
    R-Factor(R-Work) 0.3259
    R-Factor(R-Free) 0.373
    Percent Reflections(Observed) 52.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6983
    Shell Resolution(Low) 1.7198
    Number of Reflections(R-Free) 91
    Number of Reflections(R-Work) 1902
    R-Factor(R-Work) 0.3178
    R-Factor(R-Free) 0.4158
    Percent Reflections(Observed) 64.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7198
    Shell Resolution(Low) 1.7424
    Number of Reflections(R-Free) 118
    Number of Reflections(R-Work) 2157
    R-Factor(R-Work) 0.3051
    R-Factor(R-Free) 0.3408
    Percent Reflections(Observed) 74.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7424
    Shell Resolution(Low) 1.7663
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2462
    R-Factor(R-Work) 0.2906
    R-Factor(R-Free) 0.2904
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7663
    Shell Resolution(Low) 1.7915
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2716
    R-Factor(R-Work) 0.2873
    R-Factor(R-Free) 0.3109
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7915
    Shell Resolution(Low) 1.8182
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2835
    R-Factor(R-Work) 0.2766
    R-Factor(R-Free) 0.2813
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8182
    Shell Resolution(Low) 1.8467
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2874
    R-Factor(R-Work) 0.2548
    R-Factor(R-Free) 0.309
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8467
    Shell Resolution(Low) 1.8769
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2927
    R-Factor(R-Work) 0.2307
    R-Factor(R-Free) 0.3275
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8769
    Shell Resolution(Low) 1.9093
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2902
    R-Factor(R-Work) 0.2213
    R-Factor(R-Free) 0.2615
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9093
    Shell Resolution(Low) 1.944
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2938
    R-Factor(R-Work) 0.2085
    R-Factor(R-Free) 0.272
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.944
    Shell Resolution(Low) 1.9814
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2946
    R-Factor(R-Work) 0.1996
    R-Factor(R-Free) 0.2538
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9814
    Shell Resolution(Low) 2.0219
    Number of Reflections(R-Free) 170
    Number of Reflections(R-Work) 2895
    R-Factor(R-Work) 0.1906
    R-Factor(R-Free) 0.2346
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0219
    Shell Resolution(Low) 2.0658
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2949
    R-Factor(R-Work) 0.1873
    R-Factor(R-Free) 0.2543
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0658
    Shell Resolution(Low) 2.1139
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 2944
    R-Factor(R-Work) 0.1724
    R-Factor(R-Free) 0.2355
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1139
    Shell Resolution(Low) 2.1667
    Number of Reflections(R-Free) 183
    Number of Reflections(R-Work) 2901
    R-Factor(R-Work) 0.1705
    R-Factor(R-Free) 0.2222
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1667
    Shell Resolution(Low) 2.2253
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2950
    R-Factor(R-Work) 0.1601
    R-Factor(R-Free) 0.1948
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2253
    Shell Resolution(Low) 2.2908
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2956
    R-Factor(R-Work) 0.1651
    R-Factor(R-Free) 0.2333
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2908
    Shell Resolution(Low) 2.3647
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2954
    R-Factor(R-Work) 0.1624
    R-Factor(R-Free) 0.1907
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3647
    Shell Resolution(Low) 2.4492
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2944
    R-Factor(R-Work) 0.1799
    R-Factor(R-Free) 0.214
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4492
    Shell Resolution(Low) 2.5473
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2933
    R-Factor(R-Work) 0.1756
    R-Factor(R-Free) 0.2309
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5473
    Shell Resolution(Low) 2.6632
    Number of Reflections(R-Free) 165
    Number of Reflections(R-Work) 2923
    R-Factor(R-Work) 0.1782
    R-Factor(R-Free) 0.2473
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6632
    Shell Resolution(Low) 2.8036
    Number of Reflections(R-Free) 175
    Number of Reflections(R-Work) 2958
    R-Factor(R-Work) 0.1844
    R-Factor(R-Free) 0.2063
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8036
    Shell Resolution(Low) 2.9792
    Number of Reflections(R-Free) 159
    Number of Reflections(R-Work) 2948
    R-Factor(R-Work) 0.1885
    R-Factor(R-Free) 0.2431
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9792
    Shell Resolution(Low) 3.2091
    Number of Reflections(R-Free) 163
    Number of Reflections(R-Work) 2939
    R-Factor(R-Work) 0.1868
    R-Factor(R-Free) 0.207
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2091
    Shell Resolution(Low) 3.5319
    Number of Reflections(R-Free) 169
    Number of Reflections(R-Work) 2961
    R-Factor(R-Work) 0.1752
    R-Factor(R-Free) 0.2101
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5319
    Shell Resolution(Low) 4.0425
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2971
    R-Factor(R-Work) 0.149
    R-Factor(R-Free) 0.1823
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0425
    Shell Resolution(Low) 5.0916
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 3010
    R-Factor(R-Work) 0.1379
    R-Factor(R-Free) 0.1671
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0916
    Shell Resolution(Low) 40.537
    Number of Reflections(R-Free) 163
    Number of Reflections(R-Work) 3056
    R-Factor(R-Work) 0.1592
    R-Factor(R-Free) 0.1677
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.075
    f_dihedral_angle_d 13.019
    f_angle_d 1.07
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6072
    Nucleic Acid Atoms 0
    Heterogen Atoms 11
    Solvent Atoms 550
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CBASS
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution BALBES
    Structure Refinement PHENIX (phenix.refine: 1.7.1_743)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.1_743)
    model building BALBES
    data collection CBASS