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X-RAY DIFFRACTION
Materials and Methods page
4GZY
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, hanging drop
    pH 6.2
    Temperature 295.0
    Details 3.5-6% PEG 8000, 0.1M MES pH 6.1-6.3, 0.3M LiCl, 10mM MgCl2, vapor diffusion, hanging drop, temperature 295K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 207.21 α = 90
    b = 207.21 β = 90
    c = 203.22 γ = 120
     
    Space Group
    Space Group Name:    P 31 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Collection Date 2011-01-30
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X29A
    Wavelength List 1.0750
    Site NSLS
    Beamline X29A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.0
    Observed Criterion Sigma(I) 1.0
    Resolution(High) 3.5
    Resolution(Low) 50
    Number Reflections(All) 63554
    Number Reflections(Observed) 63554
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.149
    Redundancy 9.9
     
    High Resolution Shell Details
    Resolution(High) 3.5
    Resolution(Low) 3.56
    Percent Possible(All) 99.9
    Redundancy 5.5
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.5054
    Resolution(Low) 49.77
    Cut-off Sigma(F) 1.33
    Number of Reflections(all) 63554
    Number of Reflections(Observed) 63330
    Number of Reflections(R-Free) 3184
    Percent Reflections(Observed) 99.68
    R-Factor(Observed) 0.2661
    R-Work 0.2631
    R-Free 0.3217
     
    Temperature Factor Modeling
    Mean Isotropic B Value 117.367
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5054
    Shell Resolution(Low) 3.5577
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2543
    R-Factor(R-Work) 0.4001
    R-Factor(R-Free) 0.4074
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5577
    Shell Resolution(Low) 3.6133
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2584
    R-Factor(R-Work) 0.3889
    R-Factor(R-Free) 0.3838
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6133
    Shell Resolution(Low) 3.6725
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2569
    R-Factor(R-Work) 0.3844
    R-Factor(R-Free) 0.3904
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6725
    Shell Resolution(Low) 3.7358
    Number of Reflections(R-Free) 122
    Number of Reflections(R-Work) 2579
    R-Factor(R-Work) 0.3691
    R-Factor(R-Free) 0.3949
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7358
    Shell Resolution(Low) 3.8037
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2567
    R-Factor(R-Work) 0.378
    R-Factor(R-Free) 0.4219
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8037
    Shell Resolution(Low) 3.8769
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2593
    R-Factor(R-Work) 0.3408
    R-Factor(R-Free) 0.3776
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8769
    Shell Resolution(Low) 3.956
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2584
    R-Factor(R-Work) 0.322
    R-Factor(R-Free) 0.3786
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.956
    Shell Resolution(Low) 4.0419
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 2592
    R-Factor(R-Work) 0.3066
    R-Factor(R-Free) 0.3725
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0419
    Shell Resolution(Low) 4.1359
    Number of Reflections(R-Free) 108
    Number of Reflections(R-Work) 2626
    R-Factor(R-Work) 0.2831
    R-Factor(R-Free) 0.3257
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1359
    Shell Resolution(Low) 4.2393
    Number of Reflections(R-Free) 105
    Number of Reflections(R-Work) 2636
    R-Factor(R-Work) 0.2886
    R-Factor(R-Free) 0.3588
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2393
    Shell Resolution(Low) 4.3539
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2577
    R-Factor(R-Work) 0.2692
    R-Factor(R-Free) 0.3634
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3539
    Shell Resolution(Low) 4.4819
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2618
    R-Factor(R-Work) 0.2524
    R-Factor(R-Free) 0.3501
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4819
    Shell Resolution(Low) 4.6265
    Number of Reflections(R-Free) 119
    Number of Reflections(R-Work) 2616
    R-Factor(R-Work) 0.2316
    R-Factor(R-Free) 0.3007
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6265
    Shell Resolution(Low) 4.7917
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2612
    R-Factor(R-Work) 0.2355
    R-Factor(R-Free) 0.2606
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7917
    Shell Resolution(Low) 4.9834
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2623
    R-Factor(R-Work) 0.2393
    R-Factor(R-Free) 0.2906
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9834
    Shell Resolution(Low) 5.2099
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2601
    R-Factor(R-Work) 0.2535
    R-Factor(R-Free) 0.2991
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2099
    Shell Resolution(Low) 5.4843
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 2611
    R-Factor(R-Work) 0.264
    R-Factor(R-Free) 0.3188
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.4843
    Shell Resolution(Low) 5.8274
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2639
    R-Factor(R-Work) 0.2611
    R-Factor(R-Free) 0.3498
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.8274
    Shell Resolution(Low) 6.2766
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2639
    R-Factor(R-Work) 0.2596
    R-Factor(R-Free) 0.3402
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.2766
    Shell Resolution(Low) 6.9067
    Number of Reflections(R-Free) 175
    Number of Reflections(R-Work) 2616
    R-Factor(R-Work) 0.2527
    R-Factor(R-Free) 0.3286
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.9067
    Shell Resolution(Low) 7.9027
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2645
    R-Factor(R-Work) 0.2282
    R-Factor(R-Free) 0.2974
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.9027
    Shell Resolution(Low) 9.9435
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2695
    R-Factor(R-Work) 0.2063
    R-Factor(R-Free) 0.2533
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 9.9435
    Shell Resolution(Low) 49.7752
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2781
    R-Factor(R-Work) 0.2274
    R-Factor(R-Free) 0.2913
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.005
    f_chiral_restr 0.061
    f_dihedral_angle_d 15.901
    f_angle_d 0.95
    f_bond_d 0.005
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 23534
    Nucleic Acid Atoms 863
    Heterogen Atoms 3
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL
    Data Reduction (data scaling) SCALEPACK
    Structure Solution CNS
    Structure Refinement PHENIX (phenix.refine: 1.8_1069)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    molecular replacement CNS
    data reduction SCALEPACK