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X-RAY DIFFRACTION
Materials and Methods page
4GJE
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7.5
    Temperature 298.0
    Details cadmium sulphate 0.05M, sodium acetate 1.0M, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 49.63 α = 90
    b = 49.63 β = 90
    c = 116.31 γ = 120
     
    Space Group
    Space Group Name:    P 61 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type RAYONIX MX300HE
    Collection Date 2012-06-07
     
    Diffraction Radiation
    Monochromator double crystal monochromator
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type CLSI BEAMLINE 08B1-1
    Wavelength List 0.97921
    Site CLSI
    Beamline 08B1-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.6
    Resolution(Low) 50
    Number Reflections(All) 11929
    Number Reflections(Observed) 11912
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.058
    Redundancy 20.4
     
    High Resolution Shell Details
    Resolution(High) 1.6
    Resolution(Low) 1.66
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.382
    Redundancy 20.6
    Number Unique Reflections(All) 1155
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.6
    Resolution(Low) 42.98
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 11234
    Number of Reflections(Observed) 11795
    Number of Reflections(R-Free) 561
    Percent Reflections(Observed) 99.35
    R-Factor(All) 0.1219
    R-Factor(Observed) 0.122
    R-Work 0.1206
    R-Free 0.1497
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 28.3211
    Anisotropic B[1][1] 0.08
    Anisotropic B[1][2] 0.04
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.08
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.13
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.599
    Shell Resolution(Low) 1.641
    Number of Reflections(R-Free) 53
    Number of Reflections(R-Work) 782
    R-Factor(R-Work) 0.086
    R-Factor(R-Free) 0.149
    Percent Reflections(Observed) 98.93
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_rigid_bond_restr 3.425
    r_bond_refined_d 0.018
    r_angle_refined_deg 1.735
    r_dihedral_angle_1_deg 6.612
    r_dihedral_angle_2_deg 44.608
    r_dihedral_angle_3_deg 15.232
    r_dihedral_angle_4_deg 27.846
    r_chiral_restr 0.125
    r_gen_planes_refined 0.012
    r_mcbond_it 3.009
    r_mcangle_it 4.468
    r_scbond_it 6.293
    r_scangle_it 8.967
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 670
    Nucleic Acid Atoms 0
    Heterogen Atoms 21
    Solvent Atoms 67
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MxDC
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL
    Structure Solution Molrep
    Structure Refinement REFMAC 5.5.0109
     
    Software
    data extraction pdb_extract version: 3.11
    refinement REFMAC5 version: 5.5.0109
    data reduction HKL