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An Information Portal to 110790 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
2BZK
  •   Crystallization Hide
    Crystallization Experiments
    Details 0.1 M SUCCINATE PHOSPHATE GLYCINE BUFFER PH 6, 30% PEG1K, 0.5% DMSO, SITTING DROP
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 97.89 α = 90
    b = 97.89 β = 90
    c = 80.49 γ = 120
     
    Space Group
    Space Group Name:    P 65
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type RIGAKU
    Details MIRRORS
    Collection Date 2005-01-20
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU FRE
    Wavelength 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 3.0
    Resolution(High) 2.45
    Resolution(Low) 50
    Number Reflections(Observed) 16216
    Percent Possible(Observed) 99.8
    R Merge I(Observed) 0.1
    Redundancy 7.33
     
    High Resolution Shell Details
    Resolution(High) 2.45
    Resolution(Low) 2.55
    Percent Possible(All) 99.0
    R Merge I(Observed) 0.55
    Mean I Over Sigma(Observed) 3.28
    Redundancy 6.24
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.45
    Resolution(Low) 42.0
    Number of Reflections(Observed) 15369
    Number of Reflections(R-Free) 814
    Percent Reflections(Observed) 99.8
    R-Factor(Observed) 0.191
    R-Work 0.189
    R-Free 0.225
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 58.89
    Anisotropic B[1][1] 2.43
    Anisotropic B[1][2] 1.21
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 2.43
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -3.64
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.45
    Shell Resolution(Low) 2.51
    Number of Reflections(R-Free) 62
    Number of Reflections(R-Work) 1120
    R-Factor(R-Work) 0.33
    R-Factor(R-Free) 0.354
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 2.744
    r_scbond_it 1.636
    r_mcangle_it 1.056
    r_mcbond_it 0.593
    r_nbd_refined 0.207
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.005
    r_chiral_restr 0.077
    r_dihedral_angle_4_deg 15.238
    r_dihedral_angle_3_deg 14.729
    r_dihedral_angle_2_deg 33.334
    r_dihedral_angle_1_deg 6.281
    r_angle_other_deg 0.792
    r_angle_refined_deg 1.451
    r_bond_other_d 0.001
    r_bond_refined_d 0.013
    r_nbd_other 0.178
    r_nbtor_refined 0.184
    r_nbtor_other 0.084
    r_xyhbond_nbd_refined 0.153
    r_symmetry_vdw_refined 0.158
    r_symmetry_vdw_other 0.264
    r_symmetry_hbond_refined 0.171
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2223
    Nucleic Acid Atoms 0
    Heterogen Atoms 31
    Solvent Atoms 23
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHASER
    Structure Refinement REFMAC 5.2.0005
     
    Software
    refinement REFMAC version: 5.2.0005
    model building PHASER