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X-RAY DIFFRACTION
Materials and Methods page
4K5W
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8
    Temperature 277.0
    Details 32% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 47.64 α = 90
    b = 47.64 β = 90
    c = 62.66 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 1.0000
    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) 16839
    Number Reflections(Observed) 16839
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.06
    B(Isotropic) From Wilson Plot 34.7
    Redundancy 12.6
     
    High Resolution Shell Details
    Resolution(High) 1.65
    Resolution(Low) 1.68
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.255
    Mean I Over Sigma(Observed) 10.8
    Redundancy 12.9
    Number Unique Reflections(All) 825
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.65
    Resolution(Low) 47.64
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 16811
    Number of Reflections(Observed) 16811
    Number of Reflections(R-Free) 850
    Percent Reflections(Observed) 99.86
    R-Factor(All) 0.1738
    R-Factor(Observed) 0.1738
    R-Work 0.1724
    R-Free 0.2018
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 31.2719
    Anisotropic B[1][1] 0.86
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.86
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.72
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.65
    Shell Resolution(Low) 1.695
    Number of Reflections(Observed) 1192
    Number of Reflections(R-Free) 49
    Number of Reflections(R-Work) 1143
    R-Factor(R-Work) 0.214
    R-Factor(R-Free) 0.245
    Percent Reflections(Observed) 98.03
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_refined 0.014
    r_chiral_restr 0.133
    r_dihedral_angle_4_deg 8.23
    r_dihedral_angle_3_deg 16.767
    r_dihedral_angle_2_deg 35.458
    r_dihedral_angle_1_deg 6.349
    r_angle_refined_deg 1.971
    r_bond_refined_d 0.019
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1068
    Nucleic Acid Atoms 0
    Heterogen Atoms 39
    Solvent Atoms 96
     
     
  •   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