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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
2VCI
  •   Crystallization Hide
    Crystallization Experiments
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 65.14 α = 90
    b = 88.45 β = 90
    c = 99.03 γ = 90
     
    Space Group
    Space Group Name:    I 2 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type RIGAKU
    Details OSMIC BLUE
    Collection Date 2003-10-03
     
    Diffraction Radiation
    Monochromator CUK ALPHA
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU RUH3R
    Wavelength 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 2
    Resolution(Low) 30
    Number Reflections(Observed) 45746
    Percent Possible(Observed) 96.6
    R Merge I(Observed) 0.06
    Redundancy 2.38
     
    High Resolution Shell Details
    Resolution(High) 2.0
    Resolution(Low) 2.7
    Percent Possible(All) 86.1
    R Merge I(Observed) 0.38
    Mean I Over Sigma(Observed) 2.2
    Redundancy 1.75
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.0
    Resolution(Low) 29.49
    Number of Reflections(Observed) 18043
    Number of Reflections(R-Free) 976
    Percent Reflections(Observed) 96.6
    R-Factor(Observed) 0.211
    R-Work 0.207
    R-Free 0.278
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 39.99
    Anisotropic B[1][1] -0.08
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.05
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.03
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0
    Shell Resolution(Low) 2.05
    Number of Reflections(R-Free) 57
    Number of Reflections(R-Work) 1136
    R-Factor(R-Work) 0.396
    R-Factor(R-Free) 0.421
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 4.662
    r_scbond_it 3.122
    r_mcangle_it 1.899
    r_mcbond_it 1.156
    r_nbd_refined 0.227
    r_gen_planes_refined 0.008
    r_chiral_restr 0.125
    r_dihedral_angle_4_deg 25.021
    r_dihedral_angle_3_deg 16.815
    r_dihedral_angle_2_deg 37.989
    r_dihedral_angle_1_deg 6.691
    r_angle_refined_deg 1.974
    r_bond_refined_d 0.021
    r_nbtor_refined 0.316
    r_xyhbond_nbd_refined 0.186
    r_symmetry_vdw_refined 0.255
    r_symmetry_hbond_refined 0.219
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1632
    Nucleic Acid Atoms 0
    Heterogen Atoms 34
    Solvent Atoms 233
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) D*TREK
    Data Reduction (data scaling) SCALEPACK
    Structure Solution AMORE
    Structure Refinement REFMAC 5.2.0019
     
    Software
    refinement REFMAC version: 5.2.0019
    model building AMORE