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X-RAY DIFFRACTION
Materials and Methods page
3PD2
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 298.0
    Details PEG 3350, Bis-Tris, NaCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 37.23 α = 90
    b = 66.33 β = 90
    c = 93.18 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type MAR scanner 345 mm plate
    Details Osmic mirrors
    Collection Date 2009-06-25
     
    Diffraction Radiation
    Monochromator Ni FILTER
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU RUH3R
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 1.86
    Resolution(Low) 25
    Number Reflections(All) 20015
    Number Reflections(Observed) 20015
    Percent Possible(Observed) 99.5
    R Merge I(Observed) 0.055
    B(Isotropic) From Wilson Plot 13.4
    Redundancy 5.8
     
    High Resolution Shell Details
    Resolution(High) 1.86
    Resolution(Low) 1.93
    Percent Possible(All) 95.1
    R Merge I(Observed) 0.151
    Mean I Over Sigma(Observed) 9.1
    Redundancy 5.4
    Number Unique Reflections(All) 1839
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.86
    Resolution(Low) 23.85
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 19966
    Number of Reflections(R-Free) 1013
    Percent Reflections(Observed) 99.5
    R-Factor(Observed) 0.195
    R-Work 0.195
    R-Free 0.221
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 18.4
    Anisotropic B[1][1] 2.15
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 1.93
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -4.08
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.86
    Shell Resolution(Low) 1.98
    Number of Reflections(R-Free) 174
    Number of Reflections(R-Work) 3017
    R-Factor(R-Work) 0.212
    R-Factor(R-Free) 0.256
    R-Free Error 0.019
    Percent Reflections(Observed) 97.7
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_scangle_it 3.21
    c_scbond_it 2.14
    c_mcangle_it 1.7
    c_mcbond_it 1.21
    c_improper_angle_d 0.74
    c_dihedral_angle_d 23.5
    c_angle_deg 1.4
    c_bond_d 0.005
     
    Coordinate Error
    Luzzati ESD(Observed) 0.2
    Luzzati Sigma A(Observed) 0.07
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.24
    Luzzati Sigma A(R-Free Set) 0.13
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2303
    Nucleic Acid Atoms 0
    Heterogen Atoms 50
    Solvent Atoms 166
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MAR345dtb
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution MOLREP
    Structure Refinement CNS 1.1
     
    Software
    refinement CNS version: 1.1
    model building MOLREP
    data collection MAR345dtb