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X-RAY DIFFRACTION
Materials and Methods page
2VNM
  •   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 = 47.95 α = 90
    b = 76.22 β = 90
    c = 104.49 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) 1.79
    Resolution(Low) 40
    Number Reflections(Observed) 201388
    Percent Possible(Observed) 99.1
    R Merge I(Observed) 0.08
    B(Isotropic) From Wilson Plot 18.6
    Redundancy 5.5
     
    High Resolution Shell Details
    Resolution(High) 1.79
    Resolution(Low) 1.82
    Percent Possible(All) 99.7
    R Merge I(Observed) 0.47
    Mean I Over Sigma(Observed) 2.9
    Redundancy 5.4
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method OTHER
    reflnsShellList 1.79
    Resolution(Low) 61.55
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 35018
    Number of Reflections(R-Free) 1469
    Percent Reflections(Observed) 99.1
    R-Factor(Observed) 0.192
    R-Work 0.191
    R-Free 0.231
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 20.71
    Anisotropic B[1][1] 1.43
    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] -1.23
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.79
    Shell Resolution(Low) 1.84
    Number of Reflections(R-Free) 81
    Number of Reflections(R-Work) 2585
    R-Factor(R-Work) 0.252
    R-Factor(R-Free) 0.303
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.435
    r_scbond_it 2.21
    r_mcangle_it 1.479
    r_mcbond_it 0.934
    r_angle_refined_deg 1.361
    r_bond_refined_d 0.012
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2943
    Nucleic Acid Atoms 0
    Heterogen Atoms 86
    Solvent Atoms 366
     
     
  •   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