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An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
2NY0
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.6
    Temperature 298.0
    Details 7.5% PEG 8000, 7.5% MPD, 100 mM Na Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 71.89 α = 90
    b = 87.31 β = 90
    c = 196.46 γ = 90
     
    Space Group
    Space Group Name:    P 2 2 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MAR CCD 225 mm
    Collection Date 2003-10-10
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 22-ID
    Wavelength 1.0723
    Site APS
    Beamline 22-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.2
    Resolution(Low) 50
    Number Reflections(All) 63607
    Number Reflections(Observed) 54639
    Percent Possible(Observed) 85.9
    R Merge I(Observed) 0.119
    Redundancy 4.0
     
    High Resolution Shell Details
    Resolution(High) 2.2
    Resolution(Low) 2.28
    Percent Possible(All) 59.5
    R Merge I(Observed) 0.41
    Redundancy 3.6
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.2
    Resolution(Low) 48.34
    Number of Reflections(all) 63640
    Number of Reflections(Observed) 48417
    Number of Reflections(R-Free) 2591
    Percent Reflections(Observed) 80.15
    R-Factor(Observed) 0.2041
    R-Work 0.20211
    R-Free 0.2419
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 46.227
    Anisotropic B[1][1] -3.44
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 1.45
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 2.0
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2
    Shell Resolution(Low) 2.257
    Number of Reflections(R-Free) 111
    Number of Reflections(R-Work) 2235
    R-Factor(R-Work) 0.241
    R-Factor(R-Free) 0.332
    Percent Reflections(Observed) 50.46
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 0.756
    r_scbond_it 0.458
    r_mcangle_it 0.903
    r_mcbond_it 0.525
    r_nbd_refined 0.216
    r_gen_planes_refined 0.002
    r_chiral_restr 0.059
    r_dihedral_angle_4_deg 15.552
    r_dihedral_angle_3_deg 14.792
    r_dihedral_angle_2_deg 33.651
    r_dihedral_angle_1_deg 4.955
    r_angle_refined_deg 0.893
    r_bond_refined_d 0.005
    r_nbtor_refined 0.321
    r_xyhbond_nbd_refined 0.206
    r_symmetry_vdw_refined 0.203
    r_symmetry_hbond_refined 0.237
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7105
    Nucleic Acid Atoms 0
    Heterogen Atoms 176
    Solvent Atoms 381
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL
    Structure Solution CNS
    Structure Refinement REFMAC 5.2.0005
     
    Software
    data extraction pdb_extract version: 2.000
    refinement REFMAC5 version: 5.2.0005
    data processing HKL