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X-RAY DIFFRACTION
Materials and Methods page
4DJM
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 293.0
    Details protein solution: 15 mg/ml protein, 20 mM Tris pH 8.0, 200 mM NaCl, 10 % glycerol well solution: 200 mM MgCl2, 100 mM Bis-Tris pH 6.5, 25% PEG3350 protein and well solutions mixed 1:1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 59.45 α = 84.2
    b = 98.41 β = 89.8
    c = 100.88 γ = 83.8
     
    Space Group
    Space Group Name:    P 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 300 mm CCD
    Details mirrors
    Collection Date 2009-06-20
     
    Diffraction Radiation
    Monochromator Si 111 Channel
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 23-ID-D
    Wavelength List 0.9724
    Site APS
    Beamline 23-ID-D
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) -3.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.5
    Resolution(Low) 30
    Number Reflections(All) 76049
    Number Reflections(Observed) 74832
    Percent Possible(Observed) 98.4
    R Merge I(Observed) 0.109
    B(Isotropic) From Wilson Plot 51.2
    Redundancy 3.9
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.52
    Resolution(Low) 30.0
    Number of Reflections(all) 73265
    Number of Reflections(Observed) 73265
    Number of Reflections(R-Free) 1489
    Percent Reflections(Observed) 100.0
    R-Factor(All) 0.20709
    R-Factor(Observed) 0.20709
    R-Work 0.20581
    R-Free 0.26871
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic, + TLS
    Mean Isotropic B Value 47.597
    Anisotropic B[1][1] 2.0
    Anisotropic B[1][2] -0.12
    Anisotropic B[1][3] 0.87
    Anisotropic B[2][2] 1.21
    Anisotropic B[2][3] -0.67
    Anisotropic B[3][3] -3.06
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.516
    Shell Resolution(Low) 2.581
    Number of Reflections(R-Free) 90
    Number of Reflections(R-Work) 4746
    R-Factor(R-Work) 0.265
    R-Factor(R-Free) 0.372
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 9.264
    r_scbond_it 6.855
    r_mcangle_it 4.673
    r_mcbond_it 2.732
    r_gen_planes_refined 0.011
    r_chiral_restr 0.148
    r_dihedral_angle_4_deg 19.963
    r_dihedral_angle_3_deg 22.804
    r_dihedral_angle_2_deg 36.576
    r_dihedral_angle_1_deg 7.974
    r_angle_refined_deg 2.151
    r_bond_refined_d 0.023
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 12557
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Collection BluIce
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.5.0109
     
    Software
    refinement REFMAC version: 5.5.0109
    model building MOLREP
    data collection BluIce