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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4J5V
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6
    Temperature 291.0
    Details 1.7 mM ammonium sulfate, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 90.22 α = 90
    b = 90.22 β = 90
    c = 148.04 γ = 120
     
    Space Group
    Space Group Name:    H 3 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Collection Date 2010-10-25
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID23-1
    Wavelength List 0.9724
    Site ESRF
    Beamline ID23-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.15
    Resolution(Low) 30
    Number Reflections(Observed) 12580
    Percent Possible(Observed) 98.2
    R Merge I(Observed) 0.1
    Redundancy 3.1
     
    High Resolution Shell Details
    Resolution(High) 2.15
    Resolution(Low) 2.19
    Percent Possible(All) 95.9
    R Merge I(Observed) 0.134
    Redundancy 1.9
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.15
    Resolution(Low) 15.0
    Number of Reflections(Observed) 11888
    Number of Reflections(R-Free) 610
    Percent Reflections(Observed) 97.89
    R-Factor(Observed) 0.17369
    R-Work 0.17161
    R-Free 0.21401
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 45.401
    Anisotropic B[1][1] 2.22
    Anisotropic B[1][2] 1.11
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 2.22
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -3.33
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.15
    Shell Resolution(Low) 2.209
    Number of Reflections(R-Free) 47
    Number of Reflections(R-Work) 835
    R-Factor(R-Work) 0.2
    R-Factor(R-Free) 0.201
    Percent Reflections(Observed) 95.66
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.967
    r_scbond_it 2.808
    r_mcangle_it 2.127
    r_mcbond_other 0.21
    r_mcbond_it 1.287
    r_nbd_refined 0.19
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.01
    r_chiral_restr 0.144
    r_dihedral_angle_4_deg 16.44
    r_dihedral_angle_3_deg 13.944
    r_dihedral_angle_2_deg 35.564
    r_dihedral_angle_1_deg 5.575
    r_angle_refined_deg 2.114
    r_bond_refined_d 0.024
    r_nbd_other 0.207
    r_nbtor_refined 0.199
    r_nbtor_other 0.087
    r_xyhbond_nbd_refined 0.232
    r_symmetry_vdw_refined 0.215
    r_symmetry_vdw_other 0.373
    r_symmetry_hbond_refined 0.239
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 990
    Nucleic Acid Atoms 405
    Heterogen Atoms 40
    Solvent Atoms 143
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution REFMAC
    Structure Refinement REFMAC 5.5.0110
     
    Software
    data extraction pdb_extract version: 3.11
    refinement REFMAC5 version: 5.2.0019
    data reduction HKL