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X-RAY DIFFRACTION
Materials and Methods page
4I4D
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 9.5
    Temperature 289.0
    Details protein was reductively methylated, & crystallized in 0.1M CHES:NaOH pH 9.5, 30% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 73.44 α = 90
    b = 73.44 β = 90
    c = 43.33 γ = 120
     
    Space Group
    Space Group Name:    P 32 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector AREA DETECTOR
    Type ADSC QUANTUM 210r
    Collection Date 2012-07-27
     
    Diffraction Radiation
    Monochromator SAGITALLY FOCUSED Si(111)
    Diffraction Protocol single wavelength
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 19-BM
    Wavelength List 0.97931
    Site APS
    Beamline 19-BM
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.1
    Resolution(Low) 50
    Number Reflections(All) 8055
    Number Reflections(Observed) 8055
    Percent Possible(Observed) 99.7
    R Merge I(Observed) 0.07
    B(Isotropic) From Wilson Plot 44.4
    Redundancy 7.1
     
    High Resolution Shell Details
    Resolution(High) 2.1
    Resolution(Low) 2.14
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.429
    Redundancy 6.3
    Number Unique Reflections(All) 397
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 2.1
    Resolution(Low) 28.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 8041
    Number of Reflections(Observed) 8041
    Number of Reflections(R-Free) 371
    Percent Reflections(Observed) 99.48
    R-Factor(All) 0.1769
    R-Factor(Observed) 0.1769
    R-Work 0.1753
    R-Free 0.2097
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 63.4503
    Anisotropic B[1][1] 0.85
    Anisotropic B[1][2] 0.85
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.85
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -2.75
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.104
    Shell Resolution(Low) 2.158
    Number of Reflections(R-Free) 24
    Number of Reflections(R-Work) 551
    R-Factor(R-Work) 0.218
    R-Factor(R-Free) 0.225
    Percent Reflections(Observed) 97.13
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.009
    r_chiral_restr 0.087
    r_dihedral_angle_4_deg 20.985
    r_dihedral_angle_3_deg 14.904
    r_dihedral_angle_2_deg 34.229
    r_dihedral_angle_1_deg 4.659
    r_angle_other_deg 0.876
    r_angle_refined_deg 1.721
    r_bond_other_d 0.001
    r_bond_refined_d 0.016
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 643
    Nucleic Acid Atoms 0
    Heterogen Atoms 24
    Solvent Atoms 37
     
     
  •   Software and Computing Hide
    Computing
    Data Collection SBC-Collect
    Data Reduction (intensity integration) HKL-3000
    Data Reduction (data scaling) HKL-3000
    Structure Solution HKL-3000: SHELXD, SHELXE, MLPHARE, DM, SOLVE/RESOLVE, ARP/WARP, CCP4, O, COOT
    Structure Refinement REFMAC 5.7.0029
     
    Software
    data extraction pdb_extract version: 3.11
    refinement REFMAC5 version: 5.7.0029
    density modification DM version: 6.1
    phasing mlphare
    data reduction HKL