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An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1QVR
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 4.1
    Temperature 291.0
    Details PEG 4000, sodium acetate, potassium chloride, glycerol, pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 107.75 α = 90
    b = 138.48 β = 90
    c = 212.21 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 4
    Collection Date 2000-11-18
    Detector CCD
    Type BRANDEIS - B4
    Collection Date 2002-11-12
    Detector CCD
    Type SBC-2
    Collection Date 2001-03-16
     
    Diffraction Radiation
    Monochromator Si 111
    Diffraction Protocol SINGLE WAVELENGTH
    Monochromator Si 111
    Diffraction Protocol SINGLE WAVELENGTH
    Monochromator Si 220
    Diffraction Protocol MAD
     
    Diffraction Source
    Source SYNCHROTRON
    Type CHESS BEAMLINE A1
    Wavelength List 1.1
    Site CHESS
    Beamline A1
    Source SYNCHROTRON
    Type NSLS BEAMLINE X25
    Wavelength List 1.072
    Site NSLS
    Beamline X25
    Source SYNCHROTRON
    Type APS BEAMLINE 19-ID
    Wavelength List 0.9793, 0.9795, 1.0197
    Site APS
    Beamline 19-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) -3.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 3
    Resolution(Low) 48.04
    Number Reflections(All) 117313
    Number Reflections(Observed) 107224
    Percent Possible(Observed) 91.4
    B(Isotropic) From Wilson Plot 110.4
    Redundancy 2.4
     
    High Resolution Shell Details
    Resolution(High) 3.0
    Resolution(Low) 3.11
    Percent Possible(All) 37.1
    R-Sym I(Observed) 0.381
    Redundancy 1.8
    Number Unique Reflections(All) 2339
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MAD
    reflnsShellList 3.0
    Resolution(Low) 48.04
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 107224
    Number of Reflections(Observed) 102421
    Number of Reflections(R-Free) 4803
    Percent Reflections(Observed) 83.4
    R-Factor(All) 0.265
    R-Factor(Observed) 0.263
    R-Work 0.263
    R-Free 0.307
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 99.1
    Anisotropic B[1][1] -4.28
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.24
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 4.53
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0
    Shell Resolution(Low) 3.19
    Number of Reflections(R-Free) 246
    Number of Reflections(R-Work) 6585
    R-Factor(R-Work) 0.457
    R-Factor(R-Free) 0.484
    R-Free Error 0.031
    Percent Reflections(Observed) 33.4
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_scangle_it 10.99
    c_scbond_it 7.36
    c_mcangle_it 7.47
    c_mcbond_it 4.66
    c_improper_angle_d 0.86
    c_dihedral_angle_d 19.2
    c_angle_deg 1.1
    c_bond_d 0.005
     
    Coordinate Error
    Luzzati ESD(Observed) 0.51
    Luzzati Sigma A(Observed) 0.75
    Luzzati ESD(R-Free Set) 0.6
    Luzzati Sigma A(R-Free Set) 0.81
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19287
    Nucleic Acid Atoms 0
    Heterogen Atoms 209
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution CNS
    Structure Refinement CNS 1.1
     
    Software
    refinement CNS version: 1.1