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X-RAY DIFFRACTION
Materials and Methods page
2VHK
  •   Crystallization Hide
    Crystallization Experiments
    pH 7.1
    Details PROTEIN AT 45 MG/ML IN 10MM SODIUM PHOSPHATE WITH 0.25M SODIUM L-TARTRATE (PH=7.1) AND 10% (V/V) GLYCEROL; CRYSTALS GROWN AT 22C
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 57.88 α = 90
    b = 57.88 β = 90
    c = 149.95 γ = 90
     
    Space Group
    Space Group Name:    P 41 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC
    Details TOROIDAL FOCUSING MIRROR
    Collection Date 2007-08-22
     
    Diffraction Radiation
    Monochromator SI(111) CHANNEL CUT
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X6A
    Wavelength 0.8209
    Site NSLS
    Beamline X6A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 0.94
    Resolution(Low) 20
    Number Reflections(Observed) 163884
    Percent Possible(Observed) 99.0
    R Merge I(Observed) 0.04
    Redundancy 6.1
     
    High Resolution Shell Details
    Resolution(High) 0.94
    Resolution(Low) 0.96
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.59
    Mean I Over Sigma(Observed) 3.1
    Redundancy 6.7
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 0.94
    Resolution(Low) 20.0
    Number of Reflections(Observed) 155413
    Number of Reflections(R-Free) 8230
    Percent Reflections(Observed) 98.9
    R-Factor(Observed) 0.125
    R-Work 0.124
    R-Free 0.134
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 11.59
    Anisotropic B[1][1] 0.17
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.17
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.34
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 0.94
    Shell Resolution(Low) 0.96
    Number of Reflections(R-Free) 627
    Number of Reflections(R-Work) 11400
    R-Factor(R-Work) 0.183
    R-Factor(R-Free) 0.21
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.067
    r_scbond_it 2.343
    r_mcangle_it 2.007
    r_mcbond_it 1.384
    r_nbd_refined 0.28
    r_gen_planes_refined 0.009
    r_chiral_restr 0.098
    r_dihedral_angle_4_deg 11.785
    r_dihedral_angle_3_deg 10.564
    r_dihedral_angle_2_deg 35.739
    r_dihedral_angle_1_deg 6.665
    r_angle_refined_deg 1.552
    r_bond_refined_d 0.01
    r_nbtor_refined 0.313
    r_xyhbond_nbd_refined 0.122
    r_symmetry_vdw_refined 0.227
    r_symmetry_hbond_refined 0.122
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1545
    Nucleic Acid Atoms 0
    Heterogen Atoms 38
    Solvent Atoms 414
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.2.0019
     
    Software
    refinement REFMAC version: 5.2.0019
    model building MOLREP