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X-RAY DIFFRACTION
Materials and Methods page
3VPY
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 293.0
    Details PEG, HEPES, AS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 48.56 α = 90
    b = 48.71 β = 90
    c = 54.69 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 CCD
    Type ADSC QUANTUM 315r
    Collection Date 2009-03-06
     
    Diffraction Radiation
    Diffraction Protocol MAD
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRF BEAMLINE BL17U
    Wavelength List 0.9792
    Site SSRF
    Beamline BL17U
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 1.7
    Resolution(Low) 36.37
    Number Reflections(All) 13290
    Number Reflections(Observed) 13269
    Percent Possible(Observed) 99.84
    R Merge I(Observed) 0.064
    Redundancy 7.6
     
    High Resolution Shell Details
    Resolution(High) 1.7
    Resolution(Low) 1.73
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.521
    Mean I Over Sigma(Observed) 4.3
    Redundancy 7.6
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MAD
    reflnsShellList 1.7
    Resolution(Low) 36.37
    Number of Reflections(all) 13290
    Number of Reflections(Observed) 13269
    Number of Reflections(R-Free) 1487
    Percent Reflections(Observed) 99.84
    R-Factor(Observed) 0.19204
    R-Work 0.18769
    R-Free 0.23107
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 22.617
    Anisotropic B[1][1] 0.32
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.54
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.21
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.701
    Shell Resolution(Low) 1.745
    Number of Reflections(R-Free) 118
    Number of Reflections(R-Work) 937
    R-Factor(R-Work) 0.209
    R-Factor(R-Free) 0.283
    Percent Reflections(Observed) 99.15
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 4.016
    r_scbond_it 2.562
    r_mcangle_it 1.369
    r_mcbond_it 0.85
    r_symmetry_hbond_refined 0.155
    r_bond_refined_d 0.011
    r_angle_refined_deg 1.285
    r_dihedral_angle_1_deg 6.472
    r_dihedral_angle_2_deg 35.727
    r_dihedral_angle_3_deg 13.579
    r_dihedral_angle_4_deg 14.691
    r_chiral_restr 0.091
    r_gen_planes_refined 0.006
    r_nbd_refined 0.205
    r_nbtor_refined 0.301
    r_xyhbond_nbd_refined 0.109
    r_symmetry_vdw_refined 0.18
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1162
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 140
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution SHARP
    Structure Refinement REFMAC 5.2.0019
     
    Software
    refinement REFMAC version: 5.2.0019
    model building SHARP
    data collection HKL-2000