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X-RAY DIFFRACTION
Materials and Methods page
4IU4
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7.5
    Temperature 298.0
    Details 3 uL protein solution (7.0 mg/mL delta-12-LmARG, 45 mM bicine, pH 8.5, 10 mM BEC, 90 uM manganese chloride, 4.5% v/v glycerol, 1.8 mM BME) + 3 uL precipitant solution (0.1 M HEPES, pH 7.5, 12% w/v PEG3350) equilibrated against 500 uL precipitant solution, VAPOR DIFFUSION, SITTING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 88.46 α = 90
    b = 88.46 β = 90
    c = 113.96 γ = 120
     
    Space Group
    Space Group Name:    H 3
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2012-04-18
     
    Diffraction Radiation
    Monochromator Cryogenically cooled double-crystal Si(111) with horizontally focusing, sagitally bent second crystal with 4:1 magnification ratio and vertically focusing mirror
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X29A
    Wavelength List 1.075
    Site NSLS
    Beamline X29A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.8
    Resolution(Low) 50
    Number Reflections(Observed) 30860
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.099
    Redundancy 4.7
     
    High Resolution Shell Details
    Resolution(High) 1.8
    Resolution(Low) 1.86
    Percent Possible(All) 99.9
    R Merge I(Observed) 0.525
    Mean I Over Sigma(Observed) 3.455
    R-Sym I(Observed) 0.525
    Redundancy 4.3
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.8
    Resolution(Low) 50.0
    Number of Reflections(all) 30822
    Number of Reflections(Observed) 29594
    Number of Reflections(R-Free) 2260
    Percent Reflections(Observed) 96.0
    R-Factor(All) 0.1614
    R-Factor(Observed) 0.1614
    R-Work 0.1614
    R-Free 0.1932
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model ISOTROPIC
    Mean Isotropic B Value 29.0
    Anisotropic B[1][1] -5.205
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -5.205
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 10.41
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8
    Shell Resolution(Low) 1.86
    Number of Reflections(Observed) 2577
    Number of Reflections(R-Free) 204
    Percent Reflections(Observed) 84.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_improper_angle_d 0.82
    c_dihedral_angle_d 22.6
    c_angle_deg 1.4
    c_bond_d 0.007
    c_scangle_it 2.985
    c_mcangle_it 1.96
    c_scbond_it 1.983
    c_mcbond_it 1.184
     
    Coordinate Error
    Luzzati ESD(Observed) 0.24
    Luzzati Sigma A(Observed) 0.22
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.26
    Luzzati Sigma A(R-Free Set) 0.17
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2361
    Nucleic Acid Atoms 0
    Heterogen Atoms 25
    Solvent Atoms 96
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CBASS
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution CNS
    Structure Refinement CNS
     
    Software
    refinement CNS
    model building CNS
    data collection CBASS