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X-RAY DIFFRACTION
Materials and Methods page
4HYR
  •   Crystallization Hide
    Crystallization Experiments
    Method Vapor diffusion, Sitting drop
    pH 5.5
    Temperature 298.0
    Details 0.1M Bis-Tris pH 5.5, 25% PEG 3350, Vapor diffusion, Sitting drop, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 88.92 α = 90
    b = 88.92 β = 90
    c = 236.22 γ = 90
     
    Space Group
    Space Group Name:    P 41 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2011-06-16
     
    Diffraction Radiation
    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
    Resolution(High) 1.84
    Resolution(Low) 50
    Number Reflections(All) 82827
    Number Reflections(Observed) 82827
    Percent Possible(Observed) 99.5
    R Merge I(Observed) 0.116
    B(Isotropic) From Wilson Plot 22.4
    Redundancy 23.8
     
    High Resolution Shell Details
    Resolution(High) 1.84
    Resolution(Low) 1.87
    Percent Possible(All) 90.2
    R Merge I(Observed) 0.97
    Mean I Over Sigma(Observed) 3.875
    R-Sym I(Observed) 0.895
    Redundancy 22.4
    Number Unique Reflections(All) 3700
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method AB INITIO PHASING
    reflnsShellList 1.84
    Resolution(Low) 43.69
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 82357
    Number of Reflections(Observed) 82357
    Number of Reflections(R-Free) 4129
    Percent Reflections(Observed) 99.47
    R-Factor(Observed) 0.1647
    R-Work 0.1629
    R-Free 0.1997
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 26.0755
    Anisotropic B[1][1] -0.06
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.06
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.13
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.842
    Shell Resolution(Low) 1.89
    Number of Reflections(R-Free) 275
    Number of Reflections(R-Work) 5625
    R-Factor(R-Work) 0.226
    R-Factor(R-Free) 0.256
    Percent Reflections(Observed) 98.32
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_other 0.002
    r_gen_planes_refined 0.014
    r_chiral_restr 0.085
    r_dihedral_angle_4_deg 14.455
    r_dihedral_angle_3_deg 13.359
    r_dihedral_angle_2_deg 36.0
    r_dihedral_angle_1_deg 5.877
    r_angle_other_deg 0.695
    r_angle_refined_deg 1.433
    r_bond_other_d 0.0
    r_bond_refined_d 0.012
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6824
    Nucleic Acid Atoms 0
    Heterogen Atoms 27
    Solvent Atoms 528
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CBASS
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution Arp/Warp, hkl2map, PHENIX
    Structure Refinement REFMAC 5.7.0029
     
    Software
    data extraction pdb_extract version: 3.11
    refinement REFMAC5
    data reduction SCALEPACK