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An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1BVK
  •   Crystallization Hide
    Crystallization Experiments
    pH 6.5
    Details pH 6.5
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 97.7 α = 90
    b = 97.7 β = 90
    c = 174.9 γ = 90
     
    Space Group
    Space Group Name:    P 41 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 277
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type RIGAKU
    Details R-AXIS IIC
    Collection Date 1996-11
     
    Diffraction Radiation
    Monochromator GRAPHITE(002)
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU RUH2R
    Wavelength 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.7
    Resolution(Low) 50
    Number Reflections(Observed) 22379
    Percent Possible(Observed) 93.2
    R Merge I(Observed) 0.075
    B(Isotropic) From Wilson Plot 44.1
    Redundancy 5.4
     
    High Resolution Shell Details
    Resolution(High) 2.7
    Resolution(Low) 2.75
    Percent Possible(All) 73.5
    R Merge I(Observed) 0.452
    R-Sym I(Observed) 0.452
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.7
    Resolution(Low) 10.0
    Cut-off Sigma(F) 2.0
    Number of Reflections(Observed) 18822
    Number of Reflections(R-Free) 1895
    Percent Reflections(Observed) 80.3
    R-Factor(Observed) 0.208
    R-Work 0.208
    R-Free 0.297
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 31.1
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7
    Shell Resolution(Low) 2.82
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 1317
    R-Factor(R-Work) 0.326
    R-Factor(R-Free) 0.38
    Percent Reflections(Observed) 50.8
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    x_scangle_it 11.7
    x_scbond_it 9.91
    x_mcangle_it 11.7
    x_mcbond_it 9.91
    x_improper_angle_d 1.7
    x_bond_d 0.014
    x_angle_deg 1.8
    x_dihedral_angle_d 27.3
     
    Coordinate Error
    Luzzati ESD(Observed) 0.35
    Luzzati Resolution Cutoff(Low) 10.0
    Luzzati ESD(R-Free Set) 0.45
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5488
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution X-PLOR 3.8
    Structure Refinement X-PLOR 3.8
     
    Software
    refinement X-PLOR version: 3.8
    model building X-PLOR version: 3.8
    data reduction SCALEPACK
    data collection DENZO