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X-RAY DIFFRACTION
Materials and Methods page
1NKZ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 9.3
    Temperature 289.0
    Details 1.0 M Phosphate, 2.5% Benzamidine, 0.75 % Beta-octylglucoside, 25-250 mM NaCl equilibrated against 2.3 M Ammonium Sulphate at pH 9.5, pH 9.3, VAPOR DIFFUSION, SITTING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 117.05 α = 90
    b = 117.05 β = 90
    c = 298.44 γ = 120
     
    Space Group
    Space Group Name:    H 3 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 4
    Details VERTICALLY FOCUSING 1.2M Si MIRROR, MONOCHROMATED WITH A HORIZONTALLY FOCUSED Si(111) CRYSTAL
    Collection Date 1997-06-25
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SRS BEAMLINE PX9.6
    Wavelength List 0.87
    Site SRS
    Beamline PX9.6
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2
    Resolution(Low) 33
    Number Reflections(All) 49320
    Number Reflections(Observed) 48976
    R Merge I(Observed) 0.051
    Redundancy 4.1
     
    High Resolution Shell Details
    Resolution(High) 2.0
    Resolution(Low) 2.05
    Percent Possible(All) 95.0
    R Merge I(Observed) 0.306
    Mean I Over Sigma(Observed) 2.5
    Redundancy 3.3
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 2.0
    Resolution(Low) 8.0
    Number of Reflections(all) 52374
    Number of Reflections(Observed) 48976
    Number of Reflections(R-Free) 2431
    Percent Reflections(Observed) 99.3
    R-Factor(Observed) 0.1704
    R-Work 0.16943
    R-Free 0.19006
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model Combined TLS and Isotropic refinement
    Mean Isotropic B Value 22.962
    Anisotropic B[1][1] 1.03
    Anisotropic B[1][2] 0.51
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 1.03
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.54
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0
    Shell Resolution(Low) 2.049
    Number of Reflections(R-Free) 170
    Number of Reflections(R-Work) 3408
    R-Factor(R-Work) 0.184
    R-Factor(R-Free) 0.208
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_nbtor_other 0.107
    r_nbd_other 0.269
    r_nbd_refined 0.274
    r_gen_planes_other 0.04
    r_gen_planes_refined 0.019
    r_chiral_restr 0.512
    r_dihedral_angle_1_deg 6.484
    r_angle_other_deg 1.508
    r_angle_refined_deg 1.621
    r_bond_other_d 0.014
    r_bond_refined_d 0.019
    r_xyhbond_nbd_refined 0.342
    r_symmetry_vdw_refined 0.358
    r_symmetry_vdw_other 0.369
    r_symmetry_hbond_refined 0.408
    r_mcbond_it 0.845
    r_mcangle_it 1.487
    r_scbond_it 1.941
    r_scangle_it 2.61
     
    Coordinate Error
    Luzzati ESD(Observed) 0.109
    Luzzati ESD(R-Free Set) 0.105
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2178
    Nucleic Acid Atoms 0
    Heterogen Atoms 1053
    Solvent Atoms 230
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) CCP4 (SCALA)
    Structure Solution DM
    Structure Refinement REFMAC 5.1.24
     
    Software
    refinement REFMAC version: 5.1.24
    model building DM
    data reduction SCALA
    data collection MOSFLM