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An Information Portal to 105025 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
2J2I
  •   Crystallization Hide
    Crystallization Experiments
    Details 0.2 M NA2SO4, 0.1 M BIS-TRIS-PROPANE PH 7.5, 20% PEG3350, 10% ETHYLENE-GLYCOL, 0.5% DMSO, SITTING DROP, VAPOR DIFFUSION, 277 K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 98.16 α = 90
    b = 98.16 β = 90
    c = 80.37 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 VARIMAX MIRRORS
    Collection Date 2006-04-04
     
    Diffraction Radiation
    Monochromator VARIMAX MIRRORS
    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) 1.9
    Resolution(Low) 25.09
    Number Reflections(Observed) 34673
    Percent Possible(Observed) 99.7
    R Merge I(Observed) 0.06
    Redundancy 5.27
     
    High Resolution Shell Details
    Resolution(High) 1.9
    Resolution(Low) 2.0
    Percent Possible(All) 98.4
    R Merge I(Observed) 0.5
    Mean I Over Sigma(Observed) 5.5
    Redundancy 3.91
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.9
    Resolution(Low) 85.13
    Number of Reflections(Observed) 32879
    Number of Reflections(R-Free) 1765
    Percent Reflections(Observed) 99.7
    R-Factor(Observed) 0.18
    R-Work 0.179
    R-Free 0.2
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 26.59
    Anisotropic B[1][1] 0.34
    Anisotropic B[1][2] 0.17
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.34
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.52
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9
    Shell Resolution(Low) 1.95
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2335
    R-Factor(R-Work) 0.319
    R-Factor(R-Free) 0.324
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 2.626
    r_scbond_it 1.631
    r_mcangle_it 1.207
    r_mcbond_it 0.761
    r_nbd_refined 0.202
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.004
    r_chiral_restr 0.08
    r_dihedral_angle_4_deg 15.932
    r_dihedral_angle_3_deg 11.661
    r_dihedral_angle_2_deg 33.508
    r_dihedral_angle_1_deg 5.467
    r_angle_other_deg 0.882
    r_angle_refined_deg 1.305
    r_bond_other_d 0.001
    r_bond_refined_d 0.011
    r_nbd_other 0.185
    r_nbtor_refined 0.177
    r_nbtor_other 0.08
    r_xyhbond_nbd_refined 0.148
    r_symmetry_vdw_refined 0.137
    r_symmetry_vdw_other 0.327
    r_symmetry_hbond_refined 0.198
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2183
    Nucleic Acid Atoms 0
    Heterogen Atoms 40
    Solvent Atoms 168
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHASER
    Structure Refinement REFMAC 5.2.0019
     
    Software
    refinement REFMAC version: 5.2.0019
    model building PHASER