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X-RAY DIFFRACTION
Materials and Methods page
3VPD
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.5
    Temperature 293.0
    Details 2.5% PEG 400, 1.0M ammonium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 130.34 α = 90
    b = 130.34 β = 90
    c = 77.42 γ = 120
     
    Space Group
    Space Group Name:    P 31 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 95
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 270
    Collection Date 2010-03-05
     
    Diffraction Radiation
    Monochromator MIRROR
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type PHOTON FACTORY BEAMLINE AR-NE3A
    Wavelength List 1
    Site PHOTON FACTORY
    Beamline AR-NE3A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 1.95
    Resolution(Low) 50
    Number Reflections(All) 55332
    Number Reflections(Observed) 55332
    Percent Possible(Observed) 99.7
     
    High Resolution Shell Details
    Resolution(High) 1.95
    Resolution(Low) 1.98
    Percent Possible(All) 99.1
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.95
    Resolution(Low) 49.86
    Number of Reflections(all) 55332
    Number of Reflections(Observed) 52342
    Number of Reflections(R-Free) 2800
    Percent Reflections(Observed) 99.72
    R-Factor(Observed) 0.19845
    R-Work 0.19639
    R-Free 0.23777
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 35.891
    Anisotropic B[1][1] -0.01
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.01
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.01
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.952
    Shell Resolution(Low) 2.002
    Number of Reflections(R-Free) 199
    Number of Reflections(R-Work) 3846
    R-Factor(R-Work) 0.248
    R-Factor(R-Free) 0.261
    Percent Reflections(Observed) 99.41
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 4.248
    r_scbond_it 2.471
    r_mcangle_it 1.644
    r_mcbond_it 0.873
    r_gen_planes_refined 0.006
    r_chiral_restr 0.108
    r_dihedral_angle_4_deg 21.395
    r_dihedral_angle_3_deg 16.167
    r_dihedral_angle_2_deg 35.548
    r_dihedral_angle_1_deg 5.591
    r_angle_refined_deg 1.467
    r_bond_refined_d 0.013
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4236
    Nucleic Acid Atoms 0
    Heterogen Atoms 87
    Solvent Atoms 418
     
     
  •   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