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X-RAY DIFFRACTION
Materials and Methods page
4K5X
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 9
    Temperature 277.0
    Details 30% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 47.65 α = 90
    b = 47.65 β = 90
    c = 62.92 γ = 90
     
    Space Group
    Space Group Name:    P 41
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector PIXEL
    Type DECTRIS PILATUS 6M
    Details Meridionally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification
    Collection Date 2013-04-01
     
    Diffraction Radiation
    Monochromator Double crystal Si(111) with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X25
    Wavelength List 1.1000
    Site NSLS
    Beamline X25
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.65
    Resolution(Low) 50
    Number Reflections(All) 17052
    Number Reflections(Observed) 17052
    Percent Possible(Observed) 99.8
    R Merge I(Observed) 0.038
    B(Isotropic) From Wilson Plot 31.7
    Redundancy 12.8
     
    High Resolution Shell Details
    Resolution(High) 1.65
    Resolution(Low) 1.68
    Percent Possible(All) 99.3
    R Merge I(Observed) 0.314
    Mean I Over Sigma(Observed) 9.5
    Redundancy 12.5
    Number Unique Reflections(All) 831
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.65
    Resolution(Low) 47.65
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 17030
    Number of Reflections(Observed) 17030
    Number of Reflections(R-Free) 863
    Percent Reflections(Observed) 99.72
    R-Factor(All) 0.1882
    R-Factor(Observed) 0.1882
    R-Work 0.1868
    R-Free 0.2137
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 26.6089
    Anisotropic B[1][1] 0.84
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.84
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.69
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.65
    Shell Resolution(Low) 1.689
    Number of Reflections(Observed) 1172
    Number of Reflections(R-Free) 65
    Number of Reflections(R-Work) 1107
    R-Factor(R-Work) 0.27
    R-Factor(R-Free) 0.319
    Percent Reflections(Observed) 97.42
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_refined 0.014
    r_chiral_restr 0.139
    r_dihedral_angle_4_deg 9.795
    r_dihedral_angle_3_deg 15.833
    r_dihedral_angle_2_deg 35.914
    r_dihedral_angle_1_deg 6.548
    r_angle_refined_deg 1.971
    r_bond_refined_d 0.019
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1064
    Nucleic Acid Atoms 0
    Heterogen Atoms 47
    Solvent Atoms 93
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CBASS
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHASER
    Structure Refinement REFMAC 5.6.0117
     
    Software
    data extraction pdb_extract version: 3.11
    refinement REFMAC5
    molecular replacement Phaser version: 2.3.0
    data reduction SCALEPACK