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X-RAY DIFFRACTION
Materials and Methods page
3VNB
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 4.5
    Temperature 293.0
    Details Ammonium sulfate, citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 36.87 α = 90
    b = 61.1 β = 90
    c = 67.08 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 MAR scanner 345 mm plate
    Collection Date 2011-05-17
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    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) 1.5
    Resolution(Low) 50
    Number Reflections(All) 23600
    Number Reflections(Observed) 23590
    Percent Possible(Observed) 99.9
    Redundancy 14.1
     
    High Resolution Shell Details
    Resolution(High) 1.5
    Resolution(Low) 1.54
    Percent Possible(All) 100.0
    Redundancy 13.7
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.5
    Resolution(Low) 45.18
    Number of Reflections(Observed) 23590
    Number of Reflections(R-Free) 1262
    Percent Reflections(Observed) 99.91
    R-Factor(Observed) 0.18897
    R-Work 0.18762
    R-Free 0.21501
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 20.822
    Anisotropic B[1][1] 0.12
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -1.26
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 1.14
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.502
    Shell Resolution(Low) 1.541
    Number of Reflections(R-Free) 97
    Number of Reflections(R-Work) 1705
    R-Factor(R-Work) 0.197
    R-Factor(R-Free) 0.229
    Percent Reflections(Observed) 99.83
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.522
    r_scbond_it 2.242
    r_mcangle_it 1.346
    r_mcbond_it 0.833
    r_symmetry_hbond_refined 0.165
    r_bond_refined_d 0.008
    r_angle_refined_deg 1.136
    r_dihedral_angle_1_deg 5.108
    r_dihedral_angle_2_deg 32.053
    r_dihedral_angle_3_deg 11.461
    r_dihedral_angle_4_deg 17.603
    r_chiral_restr 0.083
    r_gen_planes_refined 0.004
    r_nbd_refined 0.19
    r_nbtor_refined 0.3
    r_xyhbond_nbd_refined 0.105
    r_symmetry_vdw_refined 0.157
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1168
    Nucleic Acid Atoms 0
    Heterogen Atoms 20
    Solvent Atoms 141
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution Molrep
    Structure Refinement REFMAC 5.2.0019
     
    Software
    refinement REFMAC version: 5.2.0019
    model building Molrep
    data collection HKL-2000