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X-RAY DIFFRACTION
Materials and Methods page
2NY4
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.6
    Temperature 298.0
    Details 7.0% PEG 8000, 8.0% MPD, 100 mM Na Citrate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 70.96 α = 90
    b = 87.96 β = 90
    c = 196.18 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 2003-02-13
     
    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
    Resolution(Low) 50
    Number Reflections(All) 83769
    Number Reflections(Observed) 82010
    Percent Possible(Observed) 97.9
    R Merge I(Observed) 0.125
    Redundancy 6.1
     
    High Resolution Shell Details
    Resolution(High) 2.0
    Resolution(Low) 2.07
    Percent Possible(All) 87.5
    R Merge I(Observed) 0.444
    Redundancy 3.8
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.0
    Resolution(Low) 42.91
    Number of Reflections(all) 83704
    Number of Reflections(Observed) 74827
    Number of Reflections(R-Free) 3989
    Percent Reflections(Observed) 94.16
    R-Factor(Observed) 0.20407
    R-Work 0.20211
    R-Free 0.24072
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 32.662
    Anisotropic B[1][1] -0.11
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.09
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.02
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0
    Shell Resolution(Low) 2.053
    Number of Reflections(R-Free) 249
    Number of Reflections(R-Work) 4467
    R-Factor(R-Work) 0.236
    R-Factor(R-Free) 0.279
    Percent Reflections(Observed) 77.25
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 1.806
    r_scbond_it 1.056
    r_mcangle_it 0.727
    r_mcbond_it 0.412
    r_nbd_refined 0.208
    r_gen_planes_refined 0.003
    r_chiral_restr 0.059
    r_dihedral_angle_4_deg 15.935
    r_dihedral_angle_3_deg 13.264
    r_dihedral_angle_2_deg 33.658
    r_dihedral_angle_1_deg 5.138
    r_angle_refined_deg 0.935
    r_bond_refined_d 0.005
    r_nbtor_refined 0.32
    r_xyhbond_nbd_refined 0.205
    r_symmetry_vdw_refined 0.174
    r_symmetry_hbond_refined 0.223
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7099
    Nucleic Acid Atoms 0
    Heterogen Atoms 213
    Solvent Atoms 512
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    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