POP-OUT | CLOSE

An Information Portal to 106082 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3VW9
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, hanging drop
    pH 7
    Temperature 293.0
    Details 25%(w/v) PEG 2000 MME, 10%(v/v) Glycerol, 0.1M Na-HEPES (pH 7.0), vapor diffusion, hanging drop, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 85.99 α = 90
    b = 66.98 β = 90
    c = 68.53 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type RIGAKU RAXIS VII
    Details Osmic VariMax mirrors
    Collection Date 2007-10-27
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU MICROMAX-007 HF
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 1.47
    Resolution(Low) 30.09
    Number Reflections(All) 60224
    Number Reflections(Observed) 60224
    Percent Possible(Observed) 89.3
    Redundancy 5.8
     
    High Resolution Shell Details
    Resolution(High) 1.47
    Resolution(Low) 1.51
    Percent Possible(All) 22.5
    R Merge I(Observed) 0.28
    Mean I Over Sigma(Observed) 2.8
    R-Sym I(Observed) 0.28
    Redundancy 1.6
    Number Unique Reflections(All) 1092
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.47
    Resolution(Low) 21.52
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 60170
    Number of Reflections(R-Free) 3040
    Percent Reflections(Observed) 88.52
    R-Factor(Observed) 0.1655
    R-Work 0.164
    R-Free 0.1928
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 20.3331
    Anisotropic B[1][1] -3.0805
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 1.8644
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 1.2161
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.47
    Shell Resolution(Low) 1.51
    Number of Reflections(R-Free) 47
    Number of Reflections(R-Work) 841
    R-Factor(R-Work) 0.2441
    R-Factor(R-Free) 0.2266
    Percent Reflections(Observed) 88.52
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    t_other_torsion 16.64
    t_omega_torsion 3.95
    t_angle_deg 1.05
    t_bond_d 0.01
     
    Coordinate Error
    Luzzati ESD(Observed) 0.155
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2775
    Nucleic Acid Atoms 0
    Heterogen Atoms 73
    Solvent Atoms 542
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CrystalClear
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement BUSTER 2.11.2
     
    Software
    data extraction pdb_extract version: 3.11
    refinement BUSTER-TNT version: BUSTER 2.11.2
    molecular replacement Phaser version: 2.1.4
    data reduction SCALA version: 3.3.15