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An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4IZ8
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6
    Temperature 277.0
    Details 23% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 31.05 α = 90
    b = 60.46 β = 93.29
    c = 38.04 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   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 2013-01-15
     
    Diffraction Radiation
    Monochromator double crystal Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X25
    Wavelength List 0.979
    Site NSLS
    Beamline X25
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.7
    Resolution(Low) 50
    Number Reflections(All) 15234
    Number Reflections(Observed) 15234
    Percent Possible(Observed) 97.7
    R Merge I(Observed) 0.059
    B(Isotropic) From Wilson Plot 34.2
    Redundancy 5.6
     
    High Resolution Shell Details
    Resolution(High) 1.7
    Resolution(Low) 1.73
    Percent Possible(All) 96.4
    R Merge I(Observed) 0.174
    Redundancy 4.1
    Number Unique Reflections(All) 773
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.7
    Resolution(Low) 37.97
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 15218
    Number of Reflections(Observed) 15218
    Number of Reflections(R-Free) 765
    Percent Reflections(Observed) 97.23
    R-Factor(All) 0.1787
    R-Factor(Observed) 0.1787
    R-Work 0.1769
    R-Free 0.2126
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 33.3254
    Anisotropic B[1][1] -2.73
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.89
    Anisotropic B[2][2] -2.11
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 4.76
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7
    Shell Resolution(Low) 1.739
    Number of Reflections(R-Free) 57
    Number of Reflections(R-Work) 1002
    R-Factor(R-Work) 0.239
    R-Factor(R-Free) 0.292
    Percent Reflections(Observed) 90.9
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.011
    r_chiral_restr 0.146
    r_dihedral_angle_4_deg 8.721
    r_dihedral_angle_3_deg 14.85
    r_dihedral_angle_2_deg 33.413
    r_dihedral_angle_1_deg 6.47
    r_angle_other_deg 0.884
    r_angle_refined_deg 1.929
    r_bond_other_d 0.001
    r_bond_refined_d 0.017
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1032
    Nucleic Acid Atoms 0
    Heterogen Atoms 26
    Solvent Atoms 81
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CBASS
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHASER
    Structure Refinement REFMAC 5.7.0029
     
    Software
    data extraction pdb_extract version: 3.11
    refinement REFMAC5
    molecular replacement Phaser version: 2.5.1
    data reduction HKL