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X-RAY DIFFRACTION
Materials and Methods page
3VYY
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 293.0
    Details PEG 8000, CaAc2, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 52.25 α = 90
    b = 78.53 β = 98.81
    c = 112.24 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 ADSC QUANTUM 315r
    Collection Date 2012-06-05
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X29A
    Wavelength List 1.007
    Site NSLS
    Beamline X29A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 2.9
    Resolution(Low) 50
    Number Reflections(All) 9520
    Number Reflections(Observed) 9511
    Percent Possible(Observed) 99.5
    Redundancy 3.2
     
    High Resolution Shell Details
    Resolution(High) 2.9
    Resolution(Low) 2.95
    Percent Possible(All) 94.7
    R-Sym I(Observed) 0.254
    Redundancy 3.7
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.9
    Resolution(Low) 37.01
    Number of Reflections(Observed) 9511
    Number of Reflections(R-Free) 481
    Percent Reflections(Observed) 99.19
    R-Factor(Observed) 0.22097
    R-Work 0.2189
    R-Free 0.26175
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 59.391
    Anisotropic B[1][1] 1.83
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 1.99
    Anisotropic B[2][2] -1.37
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.15
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.896
    Shell Resolution(Low) 2.972
    Number of Reflections(R-Free) 31
    Number of Reflections(R-Work) 640
    R-Factor(R-Work) 0.272
    R-Factor(R-Free) 0.368
    Percent Reflections(Observed) 91.92
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 1.865
    r_scbond_it 1.107
    r_mcangle_it 1.162
    r_mcbond_it 0.684
    r_symmetry_hbond_refined 0.146
    r_bond_refined_d 0.011
    r_angle_refined_deg 1.644
    r_dihedral_angle_1_deg 6.555
    r_dihedral_angle_2_deg 41.126
    r_dihedral_angle_3_deg 20.953
    r_dihedral_angle_4_deg 19.355
    r_chiral_restr 0.088
    r_gen_planes_refined 0.005
    r_nbd_refined 0.228
    r_nbtor_refined 0.305
    r_xyhbond_nbd_refined 0.145
    r_symmetry_vdw_refined 0.171
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1356
    Nucleic Acid Atoms 1060
    Heterogen Atoms 0
    Solvent Atoms 0
     
     
  •   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