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X-RAY DIFFRACTION
Materials and Methods page
1YV3
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7
    Temperature 278.0
    Details 100 mM MOPS (pH 7.0), 250 mM MgCl2, 11% PEG 8000, 1 mM TCEP, 2 mM Thymol, 1 mM MgCl2, 2 mM ADP, and 3 mM sodium vanadate, VAPOR DIFFUSION, HANGING DROP, temperature 278K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 88.11 α = 90
    b = 145.77 β = 90
    c = 152.91 γ = 90
     
    Space Group
    Space Group Name:    C 2 2 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MAR CCD 165 mm
    Collection Date 2004-08-09
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 32-ID
    Wavelength List 0.708
    Site APS
    Beamline 32-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2
    Resolution(Low) 40
    Number Reflections(Observed) 63478
    Percent Possible(Observed) 99.8
    R Merge I(Observed) 0.062
    B(Isotropic) From Wilson Plot 33.4
    Redundancy 5.8
     
    High Resolution Shell Details
    Resolution(High) 2.0
    Resolution(Low) 2.07
    Percent Possible(All) 98.2
    R Merge I(Observed) 0.269
    Mean I Over Sigma(Observed) 3.7
    Redundancy 5.1
    Number Unique Reflections(All) 63478
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.0
    Resolution(Low) 40.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 63478
    Number of Reflections(R-Free) 3388
    Percent Reflections(Observed) 99.51
    R-Factor(All) 0.17514
    R-Factor(Observed) 0.17514
    R-Work 0.17298
    R-Free 0.21498
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 20.417
    Anisotropic B[1][1] 0.29
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.51
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.8
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0
    Shell Resolution(Low) 2.046
    Number of Reflections(R-Free) 221
    Number of Reflections(R-Work) 4463
    R-Factor(R-Work) 0.256
    R-Factor(R-Free) 0.298
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 4.756
    r_scbond_it 3.059
    r_mcangle_it 2.072
    r_mcbond_it 1.174
    r_symmetry_hbond_refined 0.205
    r_symmetry_vdw_other 0.326
    r_symmetry_vdw_refined 0.126
    r_metal_ion_refined 0.25
    r_bond_refined_d 0.022
    r_bond_other_d 0.002
    r_angle_refined_deg 1.685
    r_angle_other_deg 1.07
    r_dihedral_angle_1_deg 5.928
    r_chiral_restr 0.116
    r_gen_planes_refined 0.011
    r_gen_planes_other 0.013
    r_nbd_refined 0.226
    r_nbd_other 0.248
    r_nbtor_other 0.089
    r_xyhbond_nbd_refined 0.185
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5461
    Nucleic Acid Atoms 0
    Heterogen Atoms 60
    Solvent Atoms 678
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.1.24
     
    Software
    refinement REFMAC version: 5.1.24