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An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1JYD
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.8
    Temperature 289.0
    Details Sodium cacodylate, sodium chloride, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 101.34 α = 90
    b = 101.34 β = 90
    c = 71.98 γ = 120
     
    Space Group
    Space Group Name:    H 3
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type MARRESEARCH
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SRS BEAMLINE PX9.5
    Wavelength List 0.9
    Site SRS
    Beamline PX9.5
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.7
    Resolution(Low) 40
    Number Reflections(Observed) 28189
    Percent Possible(Observed) 90.5
    B(Isotropic) From Wilson Plot 23.1
    Redundancy 2.4
     
    High Resolution Shell Details
    Resolution(High) 1.7
    Resolution(Low) 1.72
    Percent Possible(All) 91.0
    Mean I Over Sigma(Observed) 2.59
    R-Sym I(Observed) 0.405
    Number Unique Reflections(All) 1163
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.7
    Resolution(Low) 19.15
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 28189
    Number of Reflections(R-Free) 1380
    Percent Reflections(Observed) 90.3
    R-Factor(Observed) 0.251
    R-Work 0.248
    R-Free 0.27
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 26.1
    Anisotropic B[1][1] 1.02
    Anisotropic B[1][2] 1.35
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 1.02
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -2.03
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7
    Shell Resolution(Low) 1.81
    Number of Reflections(R-Free) 232
    Number of Reflections(R-Work) 4513
    R-Factor(R-Work) 0.319
    R-Factor(R-Free) 0.323
    R-Free Error 0.021
    Percent Reflections(Observed) 93.6
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_improper_angle_d 0.73
    c_dihedral_angle_d 24.4
    c_angle_deg 1.5
    c_bond_d 0.007
     
    Coordinate Error
    Luzzati ESD(Observed) 0.25
    Luzzati Sigma A(Observed) 0.2
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.27
    Luzzati Sigma A(R-Free Set) 0.19
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1407
    Nucleic Acid Atoms 0
    Heterogen Atoms 36
    Solvent Atoms 205
     
     
  •   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
    data reduction SCALEPACK
    data collection DENZO