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X-RAY DIFFRACTION
Materials and Methods page
1JVP
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.6
    Temperature 293.0
    Details PEG 4000, sodium chloride, ammonium acetate, sodium azide, Hepes, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 53.53 α = 90
    b = 71.8 β = 90
    c = 72.36 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 120
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type MARRESEARCH
    Collection Date 1998-04-06
     
    Diffraction Radiation
    Monochromator sagitally focused, channel-cut Si (111)
    Diffraction Protocol single wavelength
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE BM1A
    Wavelength List 0.873
    Site ESRF
    Beamline BM1A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.53
    Resolution(Low) 30
    Number Reflections(All) 39979
    Number Reflections(Observed) 39944
    Percent Possible(Observed) 93.5
    R Merge I(Observed) 0.046
    B(Isotropic) From Wilson Plot 19.5
    Redundancy 4.5
     
    High Resolution Shell Details
    Resolution(High) 1.53
    Resolution(Low) 1.62
    Percent Possible(All) 75.4
    R Merge I(Observed) 0.316
    Mean I Over Sigma(Observed) 2.0
    Redundancy 3.6
    Number Unique Reflections(All) 4990
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.53
    Resolution(Low) 30.0
    Cut-off Sigma(F) 2.0
    Number of Reflections(all) 38946
    Number of Reflections(Observed) 38298
    Number of Reflections(R-Free) 3864
    Percent Reflections(Observed) 89.5
    R-Factor(All) 0.215
    R-Factor(Observed) 0.21
    R-Work 0.206
    R-Free 0.253
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 24.3
    Anisotropic B[1][1] 0.0
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.0
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.0
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.53
    Shell Resolution(Low) 1.63
    Number of Reflections(R-Free) 503
    Number of Reflections(R-Work) 4573
    R-Factor(R-Work) 0.31
    R-Factor(R-Free) 0.322
    R-Free Error 0.014
    Percent Reflections(Observed) 72.3
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    x_scangle_it 3.62
    x_scbond_it 2.33
    x_mcangle_it 2.39
    x_mcbond_it 1.45
    x_improper_angle_d 0.69
    x_dihedral_angle_d 25.0
    x_angle_deg 1.7
    x_bond_d 0.008
     
    Coordinate Error
    Luzzati ESD(Observed) 0.2
    Luzzati Sigma A(Observed) 0.22
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.22
    Luzzati Sigma A(R-Free Set) 0.2
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2265
    Nucleic Acid Atoms 0
    Heterogen Atoms 18
    Solvent Atoms 264
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution AMORE
    Structure Refinement X-PLOR 3.851
     
    Software
    refinement X-PLOR(ONLINE) version: 3.851
    model building AMoRE