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An Information Portal to 108124 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1J1D
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8
    Temperature 293.0
    Details PEG3350, lithium chloride, Tris-HCl, calcium chloride, glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 42.35 α = 90
    b = 167.86 β = 101.35
    c = 69.71 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 90
     
    Diffraction Detector
    Detector CCD
    Type MAR CCD 165 mm
    Details KARKPATRIC-BOETZE TYPE RH-COATED DOUBLE MIRROR (SUPER MIRRORS)
    Collection Date 2001-12-09
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL41XU
    Wavelength List 1.0
    Site SPRING-8
    Beamline BL41XU
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.6
    Resolution(Low) 50
    Number Reflections(All) 28863
    Number Reflections(Observed) 27912
    Percent Possible(Observed) 96.7
    R Merge I(Observed) 0.042
    B(Isotropic) From Wilson Plot 76.0
    Redundancy 3.72
     
    High Resolution Shell Details
    Resolution(High) 2.6
    Resolution(Low) 2.69
    Percent Possible(All) 84.6
    R Merge I(Observed) 0.223
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MAD
    reflnsShellList 2.61
    Resolution(Low) 40.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 27881
    Number of Reflections(Observed) 27881
    Number of Reflections(R-Free) 1362
    Percent Reflections(Observed) 96.3
    R-Work 0.264
    R-Free 0.298
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 73.0
    Anisotropic B[1][1] -18.584
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -1.522
    Anisotropic B[2][2] 1.605
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 16.979
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.61
    Shell Resolution(Low) 2.7
    Number of Reflections(Observed) 2334
    Number of Reflections(R-Free) 100
    Number of Reflections(R-Work) 2234
    R-Factor(R-Work) 0.41
    R-Factor(R-Free) 0.36
    Percent Reflections(Observed) 81.3
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_scangle_it 3.125
    c_scbond_it 1.894
    c_mcangle_it 2.358
    c_mcbond_it 1.352
    c_improper_angle_d 0.75
    c_dihedral_angle_d 18.75
    c_angle_deg 1.398
    c_bond_d 0.0085
     
    Coordinate Error
    Luzzati ESD(Observed) 0.45
    Luzzati Sigma A(Observed) 0.51
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.5
    Luzzati Sigma A(R-Free Set) 0.55
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5669
    Nucleic Acid Atoms 0
    Heterogen Atoms 6
    Solvent Atoms 102
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution SHARP
    Structure Refinement CNS 1.0
     
    Software
    refinement CNS version: 1.0
    model building SHARP
    data reduction SCALEPACK
    data collection DENZO