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X-RAY DIFFRACTION
Materials and Methods page
3VHM
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, sitting drop
    pH 5
    Temperature 293.0
    Details 2.5-2.7M ammonium sulfate, 0.1M sodium citrate(pH 4.0-5.0), vapor diffusion, sitting drop, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 131.02 α = 90
    b = 73.54 β = 120.02
    c = 81.18 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type RAYONIX MX225HE
    Collection Date 2010-11-18
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL44XU
    Wavelength List 0.9
    Site SPRING-8
    Beamline BL44XU
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2
    Resolution(Low) 50
    Number Reflections(Observed) 44266
    Percent Possible(Observed) 98.2
    R Merge I(Observed) 0.068
    Redundancy 4.3
     
    High Resolution Shell Details
    Resolution(High) 2.0
    Resolution(Low) 2.03
    Percent Possible(All) 97.1
    R Merge I(Observed) 0.424
    Redundancy 4.4
    Number Unique Reflections(All) 2211
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.0
    Resolution(Low) 37.52
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 44247
    Number of Reflections(R-Free) 2228
    Percent Reflections(Observed) 98.19
    R-Factor(Observed) 0.1907
    R-Work 0.1885
    R-Free 0.2303
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 28.2242
    Anisotropic B[1][1] 0.01
    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) 2.003
    Shell Resolution(Low) 2.055
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 3055
    R-Factor(R-Work) 0.213
    R-Factor(R-Free) 0.252
    Percent Reflections(Observed) 97.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 5.876
    r_scbond_it 3.835
    r_mcangle_it 2.658
    r_mcbond_it 1.537
    r_gen_planes_refined 0.012
    r_chiral_restr 0.194
    r_dihedral_angle_4_deg 22.657
    r_dihedral_angle_3_deg 18.039
    r_dihedral_angle_2_deg 30.923
    r_dihedral_angle_1_deg 7.722
    r_angle_refined_deg 2.709
    r_bond_refined_d 0.029
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3821
    Nucleic Acid Atoms 0
    Heterogen Atoms 218
    Solvent Atoms 202
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.5.0110
     
    Software
    data extraction pdb_extract version: 3.10
    refinement REFMAC5
    molecular replacement MOLREP
    data reduction HKL