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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1VYZ
  •   Crystallization Hide
    Crystallization Experiments
    pH 7.4
    Details 10 PERCENT PEG4000, 50 MM AMMONIUN ACETATE, 50 MM HEPES PH 7.4
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 53.25 α = 90
    b = 71.91 β = 90
    c = 72.22 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-4
    Wavelength 0.8264
    Site ESRF
    Beamline ID14-4
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.2
    Resolution(Low) 30
    Number Reflections(Observed) 14353
    Percent Possible(Observed) 99.5
    R Merge I(Observed) 0.048
    B(Isotropic) From Wilson Plot 43.6
     
    High Resolution Shell Details
    Resolution(High) 2.2
    Resolution(Low) 2.28
    Percent Possible(All) 99.6
    R Merge I(Observed) 0.389
    Mean I Over Sigma(Observed) 3.3
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method OTHER
    reflnsShellList 2.21
    Resolution(Low) 21.43
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 14315
    Number of Reflections(R-Free) 714
    Percent Reflections(Observed) 99.2
    R-Work 0.238
    R-Free 0.28
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 41.9
    Anisotropic B[1][1] 0.54
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -4.16
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 3.61
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2
    Shell Resolution(Low) 2.34
    Number of Reflections(R-Free) 117
    Number of Reflections(R-Work) 2048
    R-Factor(R-Work) 0.357
    R-Factor(R-Free) 0.433
    R-Free Error 0.04
    Percent Reflections(Observed) 90.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_scangle_it 4.1
    c_scbond_it 2.85
    c_mcangle_it 3.04
    c_mcbond_it 1.94
    c_improper_angle_d 1.54
    c_bond_d 0.013
    c_angle_deg 1.5
    c_dihedral_angle_d 23.8
     
    Coordinate Error
    Luzzati ESD(Observed) 0.31
    Luzzati Sigma A(Observed) 0.2
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.4
    Luzzati Sigma A(R-Free Set) 0.25
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2246
    Nucleic Acid Atoms 0
    Heterogen Atoms 17
    Solvent Atoms 63
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (data scaling) SCALEPACK
    Structure Refinement CNX 2002
     
    Software
    refinement CNX version: 2002