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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
2VK0
  •   Crystallization Hide
    Crystallization Experiments
    pH 5.5
    Details pH 5.5
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 81.03 α = 90
    b = 81.03 β = 90
    c = 33.9 γ = 120
     
    Space Group
    Space Group Name:    H 3
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARRESEARCH
    Details MICRO FOCUS
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SLS BEAMLINE X06SA
    Wavelength 0.9786
    Site SLS
    Beamline X06SA
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.2
    Resolution(Low) 24.1
    Number Reflections(Observed) 13231
    Percent Possible(Observed) 98.8
    R Merge I(Observed) 0.07
    Redundancy 3.3
     
    High Resolution Shell Details
    Resolution(High) 2.2
    Resolution(Low) 2.3
    Percent Possible(All) 98.7
    R Merge I(Observed) 0.21
    Mean I Over Sigma(Observed) 5.7
    Redundancy 3.2
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.2
    Resolution(Low) 40.52
    Number of Reflections(Observed) 3958
    Number of Reflections(R-Free) 209
    Percent Reflections(Observed) 98.8
    R-Factor(Observed) 0.242
    R-Work 0.24
    R-Free 0.282
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 18.75
    Anisotropic B[1][1] 0.08
    Anisotropic B[1][2] 0.04
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.08
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.13
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2
    Shell Resolution(Low) 2.26
    Number of Reflections(R-Free) 15
    Number of Reflections(R-Work) 300
    R-Factor(R-Work) 0.316
    R-Factor(R-Free) 0.37
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 0.373
    r_scbond_it 0.272
    r_mcangle_it 0.189
    r_mcbond_it 0.164
    r_nbd_refined 0.158
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.002
    r_chiral_restr 0.317
    r_dihedral_angle_4_deg 8.774
    r_dihedral_angle_3_deg 17.823
    r_dihedral_angle_2_deg 37.341
    r_dihedral_angle_1_deg 5.35
    r_angle_other_deg 1.034
    r_angle_refined_deg 0.97
    r_bond_other_d 0.004
    r_bond_refined_d 0.006
    r_nbd_other 0.176
    r_nbtor_refined 0.181
    r_nbtor_other 0.086
    r_xyhbond_nbd_refined 0.106
    r_symmetry_vdw_refined 0.147
    r_symmetry_vdw_other 0.092
    r_symmetry_hbond_refined 0.066
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 766
    Nucleic Acid Atoms 0
    Heterogen Atoms 15
    Solvent Atoms 66
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution AMORE
    Structure Refinement REFMAC 5.3.0040
     
    Software
    refinement REFMAC version: 5.3.0040
    model building AMORE