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An Information Portal to 105025 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4DI2
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5
    Temperature 293.0
    Details 16% polyethylene glycol 8000, 0.1 M sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 82.7 α = 90
    b = 104.76 β = 103.87
    c = 101.56 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Collection Date 2011-05-20
     
    Diffraction Radiation
    Monochromator Double-crystal, Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ALS BEAMLINE 5.0.2
    Wavelength List 1.0000
    Site ALS
    Beamline 5.0.2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2
    Resolution(Low) 50
    Number Reflections(All) 113395
    Number Reflections(Observed) 113395
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.067
    Redundancy 3.8
     
    High Resolution Shell Details
    Resolution(High) 2.0
    Resolution(Low) 2.07
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.546
    Redundancy 3.8
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.0
    Resolution(Low) 49.33
    Number of Reflections(all) 113412
    Number of Reflections(Observed) 107626
    Number of Reflections(R-Free) 5714
    Percent Reflections(Observed) 99.94
    R-Factor(Observed) 0.19657
    R-Work 0.19482
    R-Free 0.22948
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 47.52
    Anisotropic B[1][1] -0.77
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.17
    Anisotropic B[2][2] 0.96
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.11
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0
    Shell Resolution(Low) 2.052
    Number of Reflections(R-Free) 463
    Number of Reflections(R-Work) 7892
    R-Factor(R-Work) 0.246
    R-Factor(R-Free) 0.295
    Percent Reflections(Observed) 99.98
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 1.954
    r_scbond_it 1.266
    r_mcangle_it 1.609
    r_mcbond_it 0.966
    r_nbd_refined 0.178
    r_gen_planes_refined 0.003
    r_chiral_restr 0.071
    r_dihedral_angle_4_deg 14.981
    r_dihedral_angle_3_deg 12.541
    r_dihedral_angle_2_deg 33.92
    r_dihedral_angle_1_deg 6.019
    r_angle_refined_deg 1.125
    r_bond_refined_d 0.008
    r_nbtor_refined 0.306
    r_xyhbond_nbd_refined 0.111
    r_symmetry_vdw_refined 0.199
    r_symmetry_hbond_refined 0.156
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 8826
    Nucleic Acid Atoms 0
    Heterogen Atoms 156
    Solvent Atoms 952
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHASER
    Structure Refinement REFMAC 5.2.0019
     
    Software
    data extraction pdb_extract version: 3.10
    refinement REFMAC5
    data reduction SCALEPACK