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An Information Portal to 106082 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3DVL
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 4
    Temperature 291.0
    Details SODIUM FORMATE, GLYCEROL, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 132.87 α = 90
    b = 135.58 β = 90
    c = 204.95 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Detector
    Detector CCD
    Type MARRESEARCH
    Collection Date 2002-07-10
    Detector CCD
    Type MARRESEARCH
    Collection Date 2003-06-01
     
    Diffraction Radiation
    Monochromator SI(111)
    Diffraction Protocol MAD
    Monochromator SI(220)
    Diffraction Protocol MAD
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 5ID-B
    Wavelength List 1
    Site APS
    Beamline 5ID-B
    Source SYNCHROTRON
    Type APS BEAMLINE 22-ID
    Wavelength List 1.25
    Site APS
    Beamline 22-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.8
    Resolution(Low) 30
    Number Reflections(All) 87750
    Number Reflections(Observed) 87750
    Percent Possible(Observed) 99.6
    R Merge I(Observed) 0.043
    Redundancy 9.0
     
    High Resolution Shell Details
    Resolution(High) 2.8
    Resolution(Low) 2.9
    Percent Possible(All) 99.3
    R Merge I(Observed) 0.501
    Mean I Over Sigma(Observed) 2.2
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method refinement
    reflnsShellList 2.8
    Resolution(Low) 30.0
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 79746
    Number of Reflections(Observed) 75705
    Number of Reflections(R-Free) 4041
    Percent Reflections(Observed) 89.6
    R-Work 0.2392
    R-Free 0.288
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic
    Mean Isotropic B Value 73.676
    Anisotropic B[1][1] -12.208
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -3.339
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 15.548
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_bond_d 0.021694
    c_angle_d 2.1166
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 23426
    Nucleic Acid Atoms 0
    Heterogen Atoms 378
    Solvent Atoms 66
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution RAVE, GLRF
    Structure Refinement CNS 1.0
     
    Software
    refinement CNS version: 1.0
    model building GLRF
    model building RAVE