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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
2VV3
  •   Crystallization Hide
    Crystallization Experiments
    pH 8
    Details TRIS 100MM PH 8, 0.7M NA-CITRATE, 1MM TCEP, 0.5MM EDTA, VAPOUR DIFFUSION, DARK, UNDER NITROGEN, 22 DEGREES CELSIUS
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 94.04 α = 90
    b = 61.75 β = 103.18
    c = 119.48 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC
    Collection Date 2007-11-16
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-3
    Wavelength 0.93
    Site ESRF
    Beamline ID14-3
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 2.85
    Resolution(Low) 58.12
    Number Reflections(Observed) 28148
    Percent Possible(Observed) 98.5
    R Merge I(Observed) 0.14
    B(Isotropic) From Wilson Plot 44.2
    Redundancy 2.8
     
    High Resolution Shell Details
    Resolution(High) 2.85
    Resolution(Low) 3.0
    Percent Possible(All) 99.9
    R Merge I(Observed) 0.34
    Mean I Over Sigma(Observed) 3.3
    Redundancy 2.9
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.85
    Resolution(Low) 33.61
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 28148
    Number of Reflections(R-Free) 1412
    Percent Reflections(Observed) 92.0
    R-Factor(Observed) 0.225
    R-Work 0.225
    R-Free 0.252
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 46.3
    Anisotropic B[1][1] 1.09
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 2.66
    Anisotropic B[2][2] 12.6
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -13.7
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.85
    Shell Resolution(Low) 3.03
    Number of Reflections(R-Free) 257
    Number of Reflections(R-Work) 4459
    R-Factor(R-Work) 0.321
    R-Factor(R-Free) 0.371
    R-Free Error 0.023
    Percent Reflections(Observed) 93.4
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_scangle_it 2.57
    c_scbond_it 1.63
    c_mcangle_it 2.08
    c_mcbond_it 1.19
    c_improper_angle_d 0.82
    c_bond_d 0.01
    c_angle_deg 1.2
    c_dihedral_angle_d 19.7
     
    Coordinate Error
    Luzzati ESD(Observed) 0.35
    Luzzati Sigma A(Observed) 0.46
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.41
    Luzzati Sigma A(R-Free Set) 0.52
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4025
    Nucleic Acid Atoms 0
    Heterogen Atoms 25
    Solvent Atoms 80
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement CNS 1.2
     
    Software
    refinement CNS version: 1.2
    model building PHASER