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X-RAY DIFFRACTION
Materials and Methods page
3RAK
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.5
    Temperature 291.0
    Details 5 mg/mL CDK2 protein, 3 mM inhibitor, 15% v/v PEG3350, 50 mM HEPES/NaOH, 50 mM Na/K phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 53.64 α = 90
    b = 71.41 β = 90
    c = 72.76 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 93
     
    Diffraction Detector
    Detector CCD
    Type RIGAKU SATURN 944+
    Details MIRRORS
    Collection Date 2008-06-16
     
    Diffraction Radiation
    Monochromator MIRRORS
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU MICROMAX-007 HF
    Wavelength 1.54178
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.75
    Resolution(Low) 20
    Number Reflections(All) 27433
    Number Reflections(Observed) 27433
    Percent Possible(Observed) 95.1
    R Merge I(Observed) 0.045
    B(Isotropic) From Wilson Plot 17.2
    Redundancy 6.77
     
    High Resolution Shell Details
    Resolution(High) 1.75
    Resolution(Low) 1.8
    Percent Possible(All) 92.4
    R Merge I(Observed) 0.187
    Mean I Over Sigma(Observed) 10.01
    Redundancy 6.84
    Number Unique Reflections(All) 2141
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.75
    Resolution(Low) 18.79
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 27433
    Number of Reflections(Observed) 27433
    Number of Reflections(R-Free) 1098
    Percent Reflections(Observed) 95.0
    R-Factor(Observed) 0.196
    R-Work 0.196
    R-Free 0.237
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 24.9
    Anisotropic B[1][1] -2.43
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -3.5
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 5.93
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.75
    Shell Resolution(Low) 1.86
    Number of Reflections(Observed) 4203
    Number of Reflections(R-Free) 175
    Number of Reflections(R-Work) 4203
    R-Factor(R-Work) 0.216
    R-Factor(R-Free) 0.261
    R-Free Error 0.02
    Percent Reflections(Observed) 92.5
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_scangle_it 2.6
    c_scbond_it 1.77
    c_mcangle_it 2.05
    c_mcbond_it 1.25
    c_improper_angle_d 0.91
    c_bond_d 0.009
    c_angle_deg 1.4
    c_dihedral_angle_d 22.7
     
    Coordinate Error
    Luzzati ESD(Observed) 0.19
    Luzzati Sigma A(Observed) 0.1
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.23
    Luzzati Sigma A(R-Free Set) 0.13
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2231
    Nucleic Acid Atoms 0
    Heterogen Atoms 25
    Solvent Atoms 192
     
     
  •   Software and Computing Hide
    Computing
    Data Collection StructureStudio
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XDS
    Structure Solution CNS 1.2
    Structure Refinement CNS 1.2
     
    Software
    refinement CNS version: 1.2
    model building CNS version: 1.2
    data collection StructureStudio