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X-RAY DIFFRACTION
Materials and Methods page
1NYX
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8
    Temperature 293.0
    Details Citrate, Tris, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 91.55 α = 90
    b = 62.09 β = 102.91
    c = 117.74 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type MARRESEARCH
    Collection Date 1999-07-08
     
    Diffraction Radiation
    Monochromator mirrors
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU RU300
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.0
    Observed Criterion Sigma(I) 1.0
    Resolution(High) 2.65
    Resolution(Low) 30
    Number Reflections(All) 16615
    Number Reflections(Observed) 16615
    Percent Possible(Observed) 87.8
    B(Isotropic) From Wilson Plot 12.9
     
    High Resolution Shell Details
    Resolution(High) 2.65
    Resolution(Low) 2.7
    Percent Possible(All) 45.0
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.65
    Resolution(Low) 29.97
    Cut-off Sigma(F) 1.0
    Number of Reflections(all) 18928
    Number of Reflections(Observed) 15168
    Number of Reflections(R-Free) 724
    Percent Reflections(Observed) 80.0
    R-Factor(All) 0.252
    R-Factor(Observed) 0.24
    R-Work 0.237
    R-Free 0.306
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 46.3
    Anisotropic B[1][1] 0.0
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.0
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.0
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.65
    Shell Resolution(Low) 2.82
    Number of Reflections(R-Free) 53
    Number of Reflections(R-Work) 1200
    R-Factor(R-Work) 0.363
    R-Factor(R-Free) 0.435
    R-Free Error 0.06
    Percent Reflections(Observed) 40.1
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_scangle_it 5.11
    c_scbond_it 3.3
    c_mcangle_it 3.78
    c_mcbond_it 2.28
    c_improper_angle_d 0.94
    c_dihedral_angle_d 20.4
    c_angle_deg 1.3
    c_bond_d 0.009
     
    Coordinate Error
    Luzzati ESD(Observed) 0.39
    Luzzati Sigma A(Observed) 0.6
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.54
    Luzzati Sigma A(R-Free Set) 0.66
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4146
    Nucleic Acid Atoms 0
    Heterogen Atoms 31
    Solvent Atoms 85
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution X-PLOR
    Structure Refinement CNX 2000
     
    Software
    refinement CNX version: 2000