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An Information Portal to 106082 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4DLI
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6
    Temperature 293.0
    Details 100 mM MES, 20-30% PEG4000, 50 mM n-BOG, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 66.26 α = 90
    b = 74.22 β = 90
    c = 77.92 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 90
     
    Diffraction Detector
    Detector CCD
    Type MARRESEARCH
    Details Dynamicall bendable mirror
    Collection Date 2009-05-08
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SLS BEAMLINE X10SA
    Wavelength List 1.00000
    Site SLS
    Beamline X10SA
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.91
    Resolution(Low) 45
    Number Reflections(All) 30473
    Number Reflections(Observed) 30306
    Percent Possible(Observed) 99.5
    R Merge I(Observed) 0.04
    B(Isotropic) From Wilson Plot 35.818
    Redundancy 3.97
     
    High Resolution Shell Details
    Resolution(High) 1.91
    Resolution(Low) 2.0
    Percent Possible(All) 99.8
    R Merge I(Observed) 0.401
    Mean I Over Sigma(Observed) 3.99
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.91
    Resolution(Low) 41.74
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 30473
    Number of Reflections(Observed) 30305
    Number of Reflections(R-Free) 910
    Percent Reflections(Observed) 100.0
    R-Factor(Observed) 0.2163
    R-Work 0.2151
    R-Free 0.2546
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 32.084
    Anisotropic B[1][1] 0.29
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.85
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.56
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.91
    Shell Resolution(Low) 1.96
    Number of Reflections(R-Free) 67
    Number of Reflections(R-Work) 2145
    R-Factor(R-Work) 0.315
    R-Factor(R-Free) 0.381
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 4.3
    r_scbond_it 2.685
    r_mcangle_it 1.862
    r_mcbond_it 1.031
    r_gen_planes_refined 0.007
    r_chiral_restr 0.103
    r_dihedral_angle_4_deg 19.352
    r_dihedral_angle_3_deg 15.671
    r_dihedral_angle_2_deg 34.811
    r_dihedral_angle_1_deg 5.454
    r_angle_refined_deg 1.455
    r_bond_refined_d 0.015
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2684
    Nucleic Acid Atoms 0
    Heterogen Atoms 42
    Solvent Atoms 135
     
     
  •   Software and Computing Hide
    Computing
    Data Collection XDS
    Data Reduction (intensity integration) XSCALE
    Data Reduction (data scaling) XSCALE
    Structure Solution PHASER
    Structure Refinement REFMAC 5.5.0102
     
    Software
    data extraction pdb_extract version: 3.10
    refinement REFMAC5
    molecular replacement Phaser version: 1.3.1
    data reduction Xscale