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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
2NY7
  •   Crystallization Hide
    Crystallization Experiments
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 101.96 α = 90
    b = 101.96 β = 90
    c = 298.29 γ = 120
     
    Space Group
    Space Group Name:    P 65 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 300 mm CCD
    Collection Date 2003-10-13
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 22-ID
    Wavelength 1.0000
    Site APS
    Beamline 22-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.3
    Resolution(Low) 50
    Number Reflections(All) 41973
    Number Reflections(Observed) 40798
    Percent Possible(Observed) 97.2
    R Merge I(Observed) 0.096
    Redundancy 8.8
     
    High Resolution Shell Details
    Resolution(High) 2.3
    Resolution(Low) 2.38
    Percent Possible(All) 77.5
    R Merge I(Observed) 0.755
    Redundancy 2.3
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.3
    Resolution(Low) 49.45
    Number of Reflections(all) 40751
    Number of Reflections(Observed) 36114
    Number of Reflections(R-Free) 1890
    Percent Reflections(Observed) 93.26
    R-Factor(Observed) 0.19601
    R-Work 0.19291
    R-Free 0.25503
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 62.345
    Anisotropic B[1][1] 0.04
    Anisotropic B[1][2] 0.02
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.04
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.06
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3
    Shell Resolution(Low) 2.358
    Number of Reflections(R-Free) 93
    Number of Reflections(R-Work) 1693
    R-Factor(R-Work) 0.254
    R-Factor(R-Free) 0.301
    Percent Reflections(Observed) 80.31
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 7.281
    r_scbond_it 5.296
    r_mcangle_it 3.235
    r_mcbond_it 2.174
    r_nbd_refined 0.216
    r_gen_planes_refined 0.002
    r_chiral_restr 0.056
    r_dihedral_angle_4_deg 17.829
    r_dihedral_angle_3_deg 14.657
    r_dihedral_angle_2_deg 29.691
    r_dihedral_angle_1_deg 5.18
    r_angle_refined_deg 0.852
    r_bond_refined_d 0.004
    r_nbtor_refined 0.325
    r_xyhbond_nbd_refined 0.238
    r_symmetry_vdw_refined 0.22
    r_symmetry_hbond_refined 0.205
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5687
    Nucleic Acid Atoms 0
    Heterogen Atoms 182
    Solvent Atoms 308
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution AMORE
    Structure Refinement REFMAC 5.2.0005
     
    Software
    data extraction pdb_extract version: 2.000
    refinement REFMAC5 version: 5.2.0005
    data processing HKL