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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
2D3E
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 5.2
    Temperature 293.0
    Details MPD, AMMONIUM ACETATE, SODIUM CITRATE, pH 5.20, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 39.08 α = 101.49
    b = 46.86 β = 101.66
    c = 95.26 γ = 90.13
     
    Space Group
    Space Group Name:    P 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 90
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 210
    Collection Date 2005-04-13
     
    Diffraction Radiation
    Monochromator SI(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL44B2
    Wavelength 1.0000
    Wavelength List 1.0000
    Site SPRING-8
    Beamline BL44B2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.6
    Resolution(Low) 45.67
    Number Reflections(All) 19366
    Number Reflections(Observed) 19366
    Percent Possible(Observed) 97.4
    R Merge I(Observed) 0.06
    B(Isotropic) From Wilson Plot 83.7
    Redundancy 16.56
     
    High Resolution Shell Details
    Resolution(High) 2.6
    Resolution(Low) 2.69
    Percent Possible(All) 97.4
    R Merge I(Observed) 0.184
    Mean I Over Sigma(Observed) 9.0
    Redundancy 17.0
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MR
    reflnsShellList 2.6
    Resolution(Low) 45.67
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 19366
    Number of Reflections(Observed) 19366
    Number of Reflections(R-Free) 986
    R-Factor(Observed) 0.254
    R-Work 0.249
    R-Free 0.309
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 90.5
    Anisotropic B[1][1] 6.2
    Anisotropic B[1][2] -4.68
    Anisotropic B[1][3] 10.15
    Anisotropic B[2][2] -35.4
    Anisotropic B[2][3] -17.32
    Anisotropic B[3][3] 29.2
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6
    Shell Resolution(Low) 2.76
    Number of Reflections(R-Free) 170
    Number of Reflections(R-Work) 3056
    R-Factor(R-Work) 0.338
    R-Factor(R-Free) 0.398
    R-Free Error 0.03
    Percent Reflections(Observed) 97.2
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_scangle_it 12.4
    c_scbond_it 8.87
    c_mcangle_it 7.89
    c_mcbond_it 5.57
    c_improper_angle_d 0.56
    c_bond_d 0.005
    c_angle_deg 0.9
    c_dihedral_angle_d 16.1
     
    Coordinate Error
    Luzzati ESD(Observed) 0.34
    Luzzati Sigma A(Observed) 0.45
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.46
    Luzzati Sigma A(R-Free Set) 0.6
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4142
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 146
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) CRYSTALCLEAR (MSC/RIGAKU)
    Data Reduction (data scaling) CRYSTALCLEAR (MSC/RIGAKU)
    Structure Solution AMORE
    Structure Refinement CNS 1.1
     
    Software
    refinement CNS version: 1.1
    model building AMOLE
    data reduction CRYSTAL version: CLEAR
    data collection CRYSTAL version: CLEAR