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X-RAY DIFFRACTION
Materials and Methods page
3VHI
  •   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 = 130.78 α = 90
    b = 73.46 β = 120.05
    c = 81.25 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
     
    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) 1.76
    Resolution(Low) 50
    Number Reflections(Observed) 65324
    Percent Possible(Observed) 99.7
    R Merge I(Observed) 0.048
    Redundancy 3.8
     
    High Resolution Shell Details
    Resolution(High) 1.76
    Resolution(Low) 1.82
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.23
    Redundancy 3.8
    Number Unique Reflections(All) 6506
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.76
    Resolution(Low) 34.91
    Number of Reflections(Observed) 62003
    Number of Reflections(R-Free) 3308
    Percent Reflections(Observed) 99.5
    R-Factor(Observed) 0.18652
    R-Work 0.18444
    R-Free 0.22612
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 26.808
    Anisotropic B[1][1] 0.0
    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) 1.764
    Shell Resolution(Low) 1.809
    Number of Reflections(R-Free) 228
    Number of Reflections(R-Work) 4458
    R-Factor(R-Work) 0.248
    R-Factor(R-Free) 0.289
    Percent Reflections(Observed) 97.83
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 6.326
    r_scbond_it 4.21
    r_mcangle_it 2.989
    r_mcbond_it 1.824
    r_gen_planes_refined 0.015
    r_chiral_restr 0.225
    r_dihedral_angle_4_deg 22.382
    r_dihedral_angle_3_deg 15.418
    r_dihedral_angle_2_deg 29.486
    r_dihedral_angle_1_deg 7.293
    r_angle_refined_deg 2.753
    r_bond_refined_d 0.034
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3811
    Nucleic Acid Atoms 0
    Heterogen Atoms 190
    Solvent Atoms 177
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.5.0110
     
    Software
    data extraction pdb_extract version: 3.10
    refinement REFMAC5
    data reduction HKL