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An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4IU5
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8.5
    Temperature 298.0
    Details 3 uL protein solution (7.0 mg/mL delta-12-LmARG, 45 mM bicine, pH 8.5, 10 mM DL-alpha-difluoromethylornithine (DFMO), 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 on a siliconized cover slide, crystals grow within one week, soaked in 10 uL 50 mM L-ornithine, 0.1 M HEPPS, pH 8.5, 15% w/v PEG3350 for 23 hours, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 89.62 α = 90
    b = 89.62 β = 90
    c = 114.36 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) 1.95
    Resolution(Low) 50
    Number Reflections(All) 24954
    Number Reflections(Observed) 24877
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.077
    Redundancy 4.7
     
    High Resolution Shell Details
    Resolution(High) 1.95
    Resolution(Low) 2.02
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.624
    Mean I Over Sigma(Observed) 2.711
    R-Sym I(Observed) 0.624
    Redundancy 4.6
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.95
    Resolution(Low) 50.0
    Number of Reflections(all) 24954
    Number of Reflections(Observed) 23754
    Number of Reflections(R-Free) 2181
    Percent Reflections(Observed) 95.2
    R-Factor(All) 0.1643
    R-Factor(Observed) 0.1643
    R-Work 0.1643
    R-Free 0.2064
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model ISOTROPIC
    Mean Isotropic B Value 53.0
    Anisotropic B[1][1] -5.278
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -5.278
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 10.557
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.95
    Shell Resolution(Low) 2.02
    Number of Reflections(Observed) 1953
    Number of Reflections(R-Free) 189
    Percent Reflections(Observed) 79.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_improper_angle_d 0.87
    c_dihedral_angle_d 22.3
    c_angle_deg 1.4
    c_bond_d 0.008
    c_scangle_it 3.038
    c_mcangle_it 2.894
    c_scbond_it 1.894
    c_mcbond_it 1.616
     
    Coordinate Error
    Luzzati ESD(Observed) 0.31
    Luzzati Sigma A(Observed) 0.34
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.34
    Luzzati Sigma A(R-Free Set) 0.35
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2361
    Nucleic Acid Atoms 0
    Heterogen Atoms 17
    Solvent Atoms 68
     
     
  •   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