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X-RAY DIFFRACTION
Materials and Methods page
2NY1
  •   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 = 71.11 α = 90
    b = 88.16 β = 90
    c = 197.67 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) 1.99
    Resolution(Low) 50
    Number Reflections(All) 85067
    Number Reflections(Observed) 74094
    Percent Possible(Observed) 87.1
    R Merge I(Observed) 0.126
    Redundancy 6.2
     
    High Resolution Shell Details
    Resolution(High) 1.99
    Resolution(Low) 2.07
    Percent Possible(All) 63.2
    R Merge I(Observed) 0.58
    Redundancy 3.0
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.99
    Resolution(Low) 42.4
    Number of Reflections(all) 76499
    Number of Reflections(Observed) 66056
    Number of Reflections(R-Free) 3536
    Percent Reflections(Observed) 80.97
    R-Factor(Observed) 0.21081
    R-Work 0.20873
    R-Free 0.24975
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 32.259
    Anisotropic B[1][1] 0.18
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.26
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.08
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.99
    Shell Resolution(Low) 2.042
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 2325
    R-Factor(R-Work) 0.28
    R-Factor(R-Free) 0.377
    Percent Reflections(Observed) 39.39
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 1.092
    r_scbond_it 0.673
    r_mcangle_it 1.178
    r_mcbond_it 0.697
    r_nbd_refined 0.219
    r_gen_planes_refined 0.003
    r_chiral_restr 0.065
    r_dihedral_angle_4_deg 20.389
    r_dihedral_angle_3_deg 15.508
    r_dihedral_angle_2_deg 34.35
    r_dihedral_angle_1_deg 5.168
    r_angle_refined_deg 1.007
    r_bond_refined_d 0.006
    r_nbtor_refined 0.32
    r_xyhbond_nbd_refined 0.234
    r_symmetry_vdw_refined 0.202
    r_symmetry_hbond_refined 0.249
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7101
    Nucleic Acid Atoms 0
    Heterogen Atoms 219
    Solvent Atoms 532
     
     
  •   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