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X-RAY DIFFRACTION
Materials and Methods page
4DKY
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.7
    Temperature 295.0
    Details 0.1M Tris-HCl, pH 6.7, 2.5M sodium formate, 10mM MnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 55.12 α = 90
    b = 37.05 β = 115.29
    c = 64.85 γ = 90
     
    Space Group
    Space Group Name:    P 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Details Mirrors
    Collection Date 2010-10-29
     
    Diffraction Radiation
    Monochromator Double Crystal Monochromator (Cryogenically cooled)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X29A
    Wavelength List 0.979
    Site NSLS
    Beamline X29A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 2.48
    Resolution(Low) 50
    Number Reflections(All) 8601
    Number Reflections(Observed) 8546
    Percent Possible(Observed) 81.3
    R Merge I(Observed) 0.094
    Redundancy 3.8
     
    High Resolution Shell Details
    Resolution(High) 2.478
    Resolution(Low) 2.542
    Percent Possible(All) 99.0
    R Merge I(Observed) 0.575
    Redundancy 3.6
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.478
    Resolution(Low) 31.92
    Number of Reflections(Observed) 6667
    Number of Reflections(R-Free) 336
    Percent Reflections(Observed) 80.9
    R-Factor(Observed) 0.18596
    R-Work 0.18314
    R-Free 0.24786
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 55.087
    Anisotropic B[1][1] -24.93
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -3.36
    Anisotropic B[2][2] -9.9
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 34.83
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.478
    Shell Resolution(Low) 2.542
    Number of Reflections(R-Free) 18
    Number of Reflections(R-Work) 214
    R-Factor(R-Work) 0.228
    R-Factor(R-Free) 0.313
    Percent Reflections(Observed) 38.16
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_other 0.007
    r_gen_planes_refined 0.008
    r_chiral_restr 0.133
    r_dihedral_angle_4_deg 18.191
    r_dihedral_angle_3_deg 22.732
    r_dihedral_angle_2_deg 38.065
    r_dihedral_angle_1_deg 7.227
    r_angle_other_deg 3.844
    r_angle_refined_deg 2.39
    r_bond_other_d 0.003
    r_bond_refined_d 0.026
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1506
    Nucleic Acid Atoms 0
    Heterogen Atoms 2
    Solvent Atoms 42
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CBASS
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHASER
    Structure Refinement REFMAC 5.6.0117
     
    Software
    data extraction pdb_extract version: 3.10
    refinement REFMAC5
    molecular replacement Phaser version: 2.3.0
    data reduction SCALEPACK
    data collection DENZO