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X-RAY DIFFRACTION
Materials and Methods page
3VYX
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7
    Temperature 293.0
    Details PEG 4000, KNO3, Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 63.2 α = 90
    b = 63.2 β = 90
    c = 107.62 γ = 90
     
    Space Group
    Space Group Name:    P 43 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Collection Date 2010-05-29
     
    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) 2.29
    Resolution(Low) 50
    Number Reflections(All) 9800
    Number Reflections(Observed) 9800
    Percent Possible(Observed) 100.0
    Redundancy 13.8
     
    High Resolution Shell Details
    Resolution(High) 2.3
    Resolution(Low) 2.34
    Percent Possible(All) 100.0
    R-Sym I(Observed) 0.322
    Redundancy 12.5
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.29
    Resolution(Low) 41.27
    Number of Reflections(all) 9800
    Number of Reflections(Observed) 9800
    Number of Reflections(R-Free) 497
    Percent Reflections(Observed) 99.87
    R-Factor(Observed) 0.19639
    R-Work 0.1931
    R-Free 0.26312
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 33.826
    Anisotropic B[1][1] 1.29
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 1.29
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -2.57
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.294
    Shell Resolution(Low) 2.354
    Number of Reflections(R-Free) 38
    Number of Reflections(R-Work) 696
    R-Factor(R-Work) 0.218
    R-Factor(R-Free) 0.362
    Percent Reflections(Observed) 99.06
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 2.698
    r_scbond_it 1.932
    r_mcangle_it 1.524
    r_mcbond_it 0.959
    r_symmetry_hbond_refined 0.213
    r_bond_refined_d 0.015
    r_angle_refined_deg 1.715
    r_dihedral_angle_1_deg 6.694
    r_dihedral_angle_2_deg 34.245
    r_dihedral_angle_3_deg 17.337
    r_dihedral_angle_4_deg 25.845
    r_chiral_restr 0.099
    r_gen_planes_refined 0.008
    r_nbd_refined 0.191
    r_nbtor_refined 0.286
    r_xyhbond_nbd_refined 0.193
    r_symmetry_vdw_refined 0.133
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 765
    Nucleic Acid Atoms 432
    Heterogen Atoms 0
    Solvent Atoms 82
     
     
  •   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