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X-RAY DIFFRACTION
Materials and Methods page
2NY5
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.6
    Temperature 298.0
    Details 9.2% PEG 4000, 9.5% MPD, 100 mM Na Citrate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 73.26 α = 90
    b = 87.64 β = 90
    c = 197.33 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 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 0.9794
    Site APS
    Beamline 22-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.5
    Resolution(Low) 50
    Number Reflections(All) 44210
    Number Reflections(Observed) 37534
    Percent Possible(Observed) 84.9
    R Merge I(Observed) 0.163
    Redundancy 3.9
     
    High Resolution Shell Details
    Resolution(High) 2.5
    Resolution(Low) 2.59
    Percent Possible(All) 62.9
    R Merge I(Observed) 0.478
    Redundancy 2.7
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.5
    Resolution(Low) 48.97
    Number of Reflections(all) 44887
    Number of Reflections(Observed) 34804
    Number of Reflections(R-Free) 1828
    Percent Reflections(Observed) 81.61
    R-Factor(Observed) 0.2007
    R-Work 0.19792
    R-Free 0.25488
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 39.921
    Anisotropic B[1][1] -0.07
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.03
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.04
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5
    Shell Resolution(Low) 2.564
    Number of Reflections(R-Free) 61
    Number of Reflections(R-Work) 1160
    R-Factor(R-Work) 0.32
    R-Factor(R-Free) 0.391
    Percent Reflections(Observed) 37.33
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 0.612
    r_scbond_it 0.377
    r_mcangle_it 0.799
    r_mcbond_it 0.458
    r_nbd_refined 0.22
    r_gen_planes_refined 0.002
    r_chiral_restr 0.056
    r_dihedral_angle_4_deg 16.074
    r_dihedral_angle_3_deg 14.854
    r_dihedral_angle_2_deg 33.282
    r_dihedral_angle_1_deg 4.683
    r_angle_refined_deg 0.883
    r_bond_refined_d 0.006
    r_nbtor_refined 0.323
    r_xyhbond_nbd_refined 0.246
    r_symmetry_vdw_refined 0.176
    r_symmetry_hbond_refined 0.208
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7078
    Nucleic Acid Atoms 0
    Heterogen Atoms 149
    Solvent Atoms 320
     
     
  •   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