POP-OUT | CLOSE

An Information Portal to 110071 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1VAT
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 5.5
    Temperature 293.0
    Details 50mg/ml HEWL, 20%(w/v) PEG4000, 100mM sodium citrate (pH 5.5), 100mM sodium iodide, and 20%(v/v) glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 78.35 α = 90
    b = 78.35 β = 90
    c = 37.54 γ = 90
     
    Space Group
    Space Group Name:    P 43 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARRESEARCH
    Collection Date 2001-04-26
     
    Diffraction Radiation
    Monochromator Si (111)
    Diffraction Protocol MAD
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL41XU
    Wavelength List 0.5400, 0.3746, 0.3734
    Site SPRING-8
    Beamline BL41XU
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.6
    Resolution(Low) 25
    Number Reflections(All) 15776
    Number Reflections(Observed) 15776
    Percent Possible(Observed) 99.5
    B(Isotropic) From Wilson Plot 16.4
    Redundancy 12.1
     
    High Resolution Shell Details
    Resolution(High) 1.6
    Resolution(Low) 1.66
    Percent Possible(All) 99.9
    Mean I Over Sigma(Observed) 5.5
    R-Sym I(Observed) 0.212
    Number Unique Reflections(All) 1539
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MAD
    reflnsShellList 1.6
    Resolution(Low) 25.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 15774
    Number of Reflections(Observed) 15774
    Number of Reflections(R-Free) 775
    Percent Reflections(Observed) 99.6
    R-Work 0.205
    R-Free 0.232
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic
    Mean Isotropic B Value 16.3
    Anisotropic B[1][1] -0.14
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.14
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.28
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6
    Shell Resolution(Low) 1.7
    Number of Reflections(Observed) 2320
    Number of Reflections(R-Free) 123
    R-Factor(R-Work) 0.221
    R-Factor(R-Free) 0.284
    R-Free Error 0.019
    Percent Reflections(Observed) 93.8
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_bond_d 0.004
    c_angle_deg 1.3
     
    Coordinate Error
    Luzzati ESD(Observed) 0.18
    Luzzati Sigma A(Observed) 0.08
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.21
    Luzzati Sigma A(R-Free Set) 0.16
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 995
    Nucleic Acid Atoms 0
    Heterogen Atoms 2
    Solvent Atoms 94
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution SHARP
    Structure Refinement CNS
     
    Software
    refinement CNS
    model building SHARP
    data reduction SCALEPACK
    data collection HKL-2000