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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
2VNN
  •   Crystallization Hide
    Crystallization Experiments
    Details CRYSTALS GROWN BY VAPOUR DIFFUSION AT 20C USING STREAK SEEDING, WITH 10% PEG8000 AND 0.1M GLYCINE PH 3.2
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 48.47 α = 90
    b = 76.7 β = 90
    c = 104.17 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC
    Collection Date 2007-10-03
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID23-1
    Wavelength 1.0723
    Site ESRF
    Beamline ID23-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.87
    Resolution(Low) 40
    Number Reflections(Observed) 176192
    Percent Possible(Observed) 99.8
    R Merge I(Observed) 0.07
    B(Isotropic) From Wilson Plot 18.7
    Redundancy 5.4
     
    High Resolution Shell Details
    Resolution(High) 1.87
    Resolution(Low) 1.9
    Percent Possible(All) 99.8
    R Merge I(Observed) 0.44
    Mean I Over Sigma(Observed) 4.4
    Redundancy 5.3
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method OTHER
    reflnsShellList 1.87
    Resolution(Low) 61.78
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 31345
    Number of Reflections(R-Free) 1338
    Percent Reflections(Observed) 99.8
    R-Factor(Observed) 0.174
    R-Work 0.173
    R-Free 0.211
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 21.8
    Anisotropic B[1][1] 1.82
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.2
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.63
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.87
    Shell Resolution(Low) 1.92
    Number of Reflections(R-Free) 102
    Number of Reflections(R-Work) 2240
    R-Factor(R-Work) 0.22
    R-Factor(R-Free) 0.26
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.564
    r_scbond_it 2.217
    r_mcangle_it 1.498
    r_mcbond_it 0.9
    r_angle_refined_deg 1.417
    r_bond_refined_d 0.012
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2943
    Nucleic Acid Atoms 0
    Heterogen Atoms 44
    Solvent Atoms 382
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Refinement REFMAC 5.3.0006
     
    Software
    refinement REFMAC version: 5.3.0006