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An Information Portal to 110790 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
2VKM
  •   Crystallization Hide
    Crystallization Experiments
    pH 6.5
    Details 12% PEG 8000, NACACODYLATE BUFFER, PH 6.5. 15MG/ML PROTEIN CONCENTRATION. ROOM TEMPERATURE.
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 86.7 α = 90
    b = 130.31 β = 97.41
    c = 87.71 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type MARRESEARCH
    Details MIRRORS
    Collection Date 2005-01-30
     
    Diffraction Radiation
    Monochromator NI FILTER
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Wavelength 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.05
    Resolution(Low) 50
    Number Reflections(Observed) 119992
    Percent Possible(Observed) 99.0
    R Merge I(Observed) 0.07
    B(Isotropic) From Wilson Plot 17.2
    Redundancy 3.9
     
    High Resolution Shell Details
    Resolution(High) 2.01
    Resolution(Low) 2.12
    Percent Possible(All) 95.0
    R Merge I(Observed) 0.39
    Mean I Over Sigma(Observed) 2.7
    Redundancy 2.5
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.05
    Resolution(Low) 50.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 113913
    Number of Reflections(R-Free) 9156
    Percent Reflections(Observed) 94.3
    R-Factor(Observed) 0.2016
    R-Work 0.2016
    R-Free 0.2418
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 29.4
    Anisotropic B[1][1] 2.717
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 2.956
    Anisotropic B[2][2] 5.072
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -7.789
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0
    Shell Resolution(Low) 2.13
    Number of Reflections(R-Free) 836
    Number of Reflections(R-Work) 9419
    R-Factor(R-Work) 0.273
    R-Factor(R-Free) 0.317
    R-Free Error 0.011
    Percent Reflections(Observed) 47.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_scangle_it 2.92
    c_scbond_it 2.04
    c_mcangle_it 2.21
    c_mcbond_it 1.39
    c_improper_angle_d 0.93
    c_bond_d 0.01
    c_angle_deg 1.6
    c_dihedral_angle_d 25.5
     
    Coordinate Error
    Luzzati ESD(Observed) 0.24
    Luzzati Sigma A(Observed) 0.21
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.29
    Luzzati Sigma A(R-Free Set) 0.27
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 12212
    Nucleic Acid Atoms 0
    Heterogen Atoms 188
    Solvent Atoms 784
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution AMORE
    Structure Refinement CNS 1.0
     
    Software
    refinement CNS version: 1.0
    model building AMORE