POP-OUT | CLOSE
 
X-RAY DIFFRACTION
Materials and Methods page
3VPC
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 4.6
    Temperature 293.0
    Details 0.2M (NH4)H2PO4, 10% PEG 3350, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 63.27 α = 87.77
    b = 67.85 β = 75.29
    c = 80.03 γ = 67.03
     
    Space Group
    Space Group Name:    P 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 95
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 210r
    Collection Date 2008-11-02
     
    Diffraction Radiation
    Monochromator MIRRORS
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type PHOTON FACTORY BEAMLINE AR-NW12A
    Wavelength List 1
    Site PHOTON FACTORY
    Beamline AR-NW12A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 1.87
    Resolution(Low) 50
    Number Reflections(All) 98303
    Number Reflections(Observed) 98303
    Percent Possible(Observed) 94.4
     
    High Resolution Shell Details
    Resolution(High) 1.87
    Resolution(Low) 1.94
    Percent Possible(All) 87.8
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.87
    Resolution(Low) 34.96
    Number of Reflections(all) 89452
    Number of Reflections(Observed) 89452
    Number of Reflections(R-Free) 4707
    Percent Reflections(Observed) 95.62
    R-Factor(Observed) 0.20078
    R-Work 0.19799
    R-Free 0.25314
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 27.198
    Anisotropic B[1][1] 0.0
    Anisotropic B[1][2] -0.02
    Anisotropic B[1][3] -0.01
    Anisotropic B[2][2] 0.02
    Anisotropic B[2][3] 0.02
    Anisotropic B[3][3] 0.0
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.865
    Shell Resolution(Low) 1.914
    Number of Reflections(R-Free) 270
    Number of Reflections(R-Work) 5671
    R-Factor(R-Work) 0.268
    R-Factor(R-Free) 0.33
    Percent Reflections(Observed) 81.74
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.252
    r_scbond_it 1.96
    r_mcangle_it 1.425
    r_mcbond_it 0.782
    r_gen_planes_refined 0.005
    r_chiral_restr 0.104
    r_dihedral_angle_4_deg 17.057
    r_dihedral_angle_3_deg 16.8
    r_dihedral_angle_2_deg 40.366
    r_dihedral_angle_1_deg 6.342
    r_angle_refined_deg 1.452
    r_bond_refined_d 0.012
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 8841
    Nucleic Acid Atoms 0
    Heterogen Atoms 108
    Solvent Atoms 956
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution Phaser
    Structure Refinement REFMAC 5.5.0088
     
    Software
    refinement REFMAC version: 5.5.0088
    model building Phaser
    data collection HKL-2000