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An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
2BZJ
  •   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 = 98.89 α = 90
    b = 98.89 β = 90
    c = 81.03 γ = 120
     
    Space Group
    Space Group Name:    P 65
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARRESEARCH
    Details MIRRORS
    Collection Date 2005-04-23
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SLS BEAMLINE X10SA
    Wavelength 0.978
    Site SLS
    Beamline X10SA
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 2.05
    Resolution(Low) 50
    Number Reflections(Observed) 27388
    Percent Possible(Observed) 96.7
    R Merge I(Observed) 0.1
    Redundancy 3.3
     
    High Resolution Shell Details
    Resolution(High) 2.05
    Resolution(Low) 2.15
    Percent Possible(All) 80.0
    R Merge I(Observed) 0.44
    Mean I Over Sigma(Observed) 2.0
    Redundancy 2.0
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.05
    Resolution(Low) 85.75
    Number of Reflections(Observed) 25947
    Number of Reflections(R-Free) 1381
    Percent Reflections(Observed) 96.7
    R-Factor(Observed) 0.185
    R-Work 0.183
    R-Free 0.221
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 34.77
    Anisotropic B[1][1] 0.61
    Anisotropic B[1][2] 0.31
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.61
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.92
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.05
    Shell Resolution(Low) 2.1
    Number of Reflections(R-Free) 63
    Number of Reflections(R-Work) 1444
    R-Factor(R-Work) 0.328
    R-Factor(R-Free) 0.452
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 2.615
    r_scbond_it 1.626
    r_mcangle_it 1.364
    r_mcbond_it 0.919
    r_nbd_refined 0.184
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.005
    r_chiral_restr 0.074
    r_dihedral_angle_4_deg 14.499
    r_dihedral_angle_3_deg 13.717
    r_dihedral_angle_2_deg 33.78
    r_dihedral_angle_1_deg 5.475
    r_angle_other_deg 0.846
    r_angle_refined_deg 1.39
    r_bond_other_d 0.001
    r_bond_refined_d 0.013
    r_nbd_other 0.18
    r_nbtor_refined 0.176
    r_nbtor_other 0.081
    r_xyhbond_nbd_refined 0.154
    r_symmetry_vdw_refined 0.053
    r_symmetry_vdw_other 0.314
    r_symmetry_hbond_refined 0.132
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2213
    Nucleic Acid Atoms 0
    Heterogen Atoms 36
    Solvent Atoms 140
     
     
  •   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