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X-RAY DIFFRACTION
Materials and Methods page
3VR4
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 6.5
    Temperature 296.0
    Details 29.2% PEG3350, 0.1M NaF, 0.1M Bis-Tris propane, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 127.98 α = 90
    b = 128.48 β = 90
    c = 225.93 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
    Diffrn ID 2
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 210r
    Collection Date 2009-12-16
    Detector CCD
    Type ADSC QUANTUM 210r
    Collection Date 2009-12-16
     
    Diffraction Radiation
    Monochromator Double Crystal Si(111)
    Diffraction Protocol single wavelength
    Monochromator Double Crystal Si(111)
    Diffraction Protocol single wavelength
     
    Diffraction Source
    Source SYNCHROTRON
    Type PHOTON FACTORY BEAMLINE AR-NW12A
    Wavelength List 1.0000
    Site PHOTON FACTORY
    Beamline AR-NW12A
    Source SYNCHROTRON
    Type PHOTON FACTORY BEAMLINE AR-NW12A
    Wavelength List 0.97919
    Site PHOTON FACTORY
    Beamline AR-NW12A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) -3.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.17
    Resolution(Low) 37.12
    Number Reflections(All) 195452
    Number Reflections(Observed) 195452
    Percent Possible(Observed) 99.7
    R Merge I(Observed) 0.09
    B(Isotropic) From Wilson Plot 29.349
    Redundancy 7.4
     
    High Resolution Shell Details
    Resolution(High) 2.17
    Resolution(Low) 2.23
    Percent Possible(All) 97.1
    R Merge I(Observed) 0.535
    Mean I Over Sigma(Observed) 3.7
    Redundancy 7.2
    Number Unique Reflections(All) 13905
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT and SAD
    reflnsShellList 2.172
    Resolution(Low) 34.042
    Cut-off Sigma(F) 1.32
    Number of Reflections(Observed) 194627
    Number of Reflections(R-Free) 9799
    Percent Reflections(Observed) 98.96
    R-Factor(All) 0.1685
    R-Factor(Observed) 0.1685
    R-Work 0.1665
    R-Free 0.2108
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 32.7787
    Anisotropic B[1][1] -0.5525
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.2784
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.8309
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1731
    Shell Resolution(Low) 2.2105
    Number of Reflections(R-Free) 943
    Number of Reflections(R-Work) 17502
    R-Factor(R-Work) 0.2303
    R-Factor(R-Free) 0.2669
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2105
    Shell Resolution(Low) 2.2507
    Number of Reflections(R-Free) 946
    Number of Reflections(R-Work) 17895
    R-Factor(R-Work) 0.2263
    R-Factor(R-Free) 0.2756
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2507
    Shell Resolution(Low) 2.294
    Number of Reflections(R-Free) 943
    Number of Reflections(R-Work) 18031
    R-Factor(R-Work) 0.2226
    R-Factor(R-Free) 0.2548
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.294
    Shell Resolution(Low) 2.3408
    Number of Reflections(R-Free) 981
    Number of Reflections(R-Work) 17847
    R-Factor(R-Work) 0.2117
    R-Factor(R-Free) 0.2573
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3408
    Shell Resolution(Low) 2.3917
    Number of Reflections(R-Free) 986
    Number of Reflections(R-Work) 17861
    R-Factor(R-Work) 0.2078
    R-Factor(R-Free) 0.2546
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3917
    Shell Resolution(Low) 2.4473
    Number of Reflections(R-Free) 910
    Number of Reflections(R-Work) 18057
    R-Factor(R-Work) 0.2066
    R-Factor(R-Free) 0.2511
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4473
    Shell Resolution(Low) 2.5084
    Number of Reflections(R-Free) 962
    Number of Reflections(R-Work) 17943
    R-Factor(R-Work) 0.2039
    R-Factor(R-Free) 0.253
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5084
    Shell Resolution(Low) 2.5762
    Number of Reflections(R-Free) 878
    Number of Reflections(R-Work) 18006
    R-Factor(R-Work) 0.2011
    R-Factor(R-Free) 0.2475
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5762
    Shell Resolution(Low) 2.652
    Number of Reflections(R-Free) 973
    Number of Reflections(R-Work) 17938
    R-Factor(R-Work) 0.1916
    R-Factor(R-Free) 0.2361
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.652
    Shell Resolution(Low) 2.7375
    Number of Reflections(R-Free) 1008
    Number of Reflections(R-Work) 17957
    R-Factor(R-Work) 0.1891
    R-Factor(R-Free) 0.2422
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7375
    Shell Resolution(Low) 2.8352
    Number of Reflections(R-Free) 1041
    Number of Reflections(R-Work) 17894
    R-Factor(R-Work) 0.1819
    R-Factor(R-Free) 0.2382
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8352
    Shell Resolution(Low) 2.9486
    Number of Reflections(R-Free) 876
    Number of Reflections(R-Work) 17998
    R-Factor(R-Work) 0.1774
    R-Factor(R-Free) 0.2262
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9486
    Shell Resolution(Low) 3.0827
    Number of Reflections(R-Free) 941
    Number of Reflections(R-Work) 17963
    R-Factor(R-Work) 0.1699
    R-Factor(R-Free) 0.2269
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0827
    Shell Resolution(Low) 3.245
    Number of Reflections(R-Free) 959
    Number of Reflections(R-Work) 17949
    R-Factor(R-Work) 0.1625
    R-Factor(R-Free) 0.221
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.245
    Shell Resolution(Low) 3.4479
    Number of Reflections(R-Free) 941
    Number of Reflections(R-Work) 18005
    R-Factor(R-Work) 0.1543
    R-Factor(R-Free) 0.2174
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4479
    Shell Resolution(Low) 3.7136
    Number of Reflections(R-Free) 1004
    Number of Reflections(R-Work) 17838
    R-Factor(R-Work) 0.1397
    R-Factor(R-Free) 0.1867
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7136
    Shell Resolution(Low) 4.0863
    Number of Reflections(R-Free) 989
    Number of Reflections(R-Work) 17722
    R-Factor(R-Work) 0.1287
    R-Factor(R-Free) 0.1717
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0863
    Shell Resolution(Low) 4.6752
    Number of Reflections(R-Free) 928
    Number of Reflections(R-Work) 17635
    R-Factor(R-Work) 0.1164
    R-Factor(R-Free) 0.1535
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6752
    Shell Resolution(Low) 5.8814
    Number of Reflections(R-Free) 905
    Number of Reflections(R-Work) 17482
    R-Factor(R-Work) 0.144
    R-Factor(R-Free) 0.1697
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.8814
    Shell Resolution(Low) 28.0517
    Number of Reflections(R-Free) 835
    Number of Reflections(R-Work) 16955
    R-Factor(R-Work) 0.1731
    R-Factor(R-Free) 0.2014
    Percent Reflections(Observed) 90.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 12.97
    f_plane_restr 0.003
    f_chiral_restr 0.051
    f_angle_d 0.738
    f_bond_d 0.003
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 26189
    Nucleic Acid Atoms 0
    Heterogen Atoms 87
    Solvent Atoms 1795
     
     
  •   Software and Computing Hide
    Computing
    Data Collection UGUI
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XDS
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: dev_934)
     
    Software
    refinement PHENIX version: (phenix.refine: dev_934)
    model building PHASER
    data collection UGUI