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An Information Portal to 106858 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
2XVD
  •   Crystallization Hide
    Crystallization Experiments
    pH 7.5
    Details PH 7.5
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 46.71 α = 90
    b = 53.31 β = 111.75
    c = 61.33 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type RIGAKU
    Details MIRRORS
    Collection Date 2006-09-13
     
    Diffraction Radiation
    Monochromator NI FILTER
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU MM007
    Wavelength 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 1.7
    Resolution(Low) 43
    Number Reflections(Observed) 28154
    Percent Possible(Observed) 90.9
    R Merge I(Observed) 0.05
    B(Isotropic) From Wilson Plot 23.9
    Redundancy 3.32
     
    High Resolution Shell Details
    Resolution(High) 1.7
    Resolution(Low) 1.76
    Percent Possible(All) 46.9
    R Merge I(Observed) 0.36
    Mean I Over Sigma(Observed) 2.0
    Redundancy 2.06
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.7
    Resolution(Low) 43.05
    Number of Reflections(Observed) 26740
    Number of Reflections(R-Free) 1414
    Percent Reflections(Observed) 90.91
    R-Factor(Observed) 0.17687
    R-Work 0.1751
    R-Free 0.20913
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 30.912
    Anisotropic B[1][1] -0.3
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -0.44
    Anisotropic B[2][2] -0.41
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.38
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7
    Shell Resolution(Low) 1.744
    Number of Reflections(R-Free) 51
    Number of Reflections(R-Work) 940
    R-Factor(R-Work) 0.288
    R-Factor(R-Free) 0.281
    Percent Reflections(Observed) 43.66
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.365
    r_scbond_it 2.11
    r_mcangle_it 1.439
    r_mcbond_other 0.193
    r_mcbond_it 0.792
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.006
    r_chiral_restr 0.091
    r_dihedral_angle_4_deg 20.647
    r_dihedral_angle_3_deg 12.259
    r_dihedral_angle_2_deg 36.679
    r_dihedral_angle_1_deg 5.681
    r_angle_other_deg 0.945
    r_angle_refined_deg 1.436
    r_bond_other_d 0.001
    r_bond_refined_d 0.015
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2072
    Nucleic Acid Atoms 0
    Heterogen Atoms 39
    Solvent Atoms 217
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) D*TREK
    Data Reduction (data scaling) D*TREK
    Structure Solution AMORE
    Structure Refinement REFMAC 5.5.0109
     
    Software
    refinement REFMAC version: 5.5.0109
    model building AMORE