3PY0

CDK2 in complex with inhibitor SU9516


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52915 mg/mL CDK2, 1.5 mM SU9516, 15% (v/v) PEG3350, 50 mM HEPES/NaOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
238.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.54α = 90
b = 71.92β = 90
c = 72.28γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93IMAGE PLATERIGAKUMIRRORS2010-10-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.752099.50.0517.542870128701-320.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.899.80.274542316

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1PW21.7518.752870128701109199.50.2120.2120.26RANDOM31.1
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-3.2-5.378.57
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.3
c_scangle_it2.57
c_mcangle_it2.24
c_scbond_it1.66
c_angle_deg1.5
c_mcbond_it1.34
c_improper_angle_d0.9
c_bond_d0.01
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.3
c_scangle_it2.57
c_mcangle_it2.24
c_scbond_it1.66
c_angle_deg1.5
c_mcbond_it1.34
c_improper_angle_d0.9
c_bond_d0.01
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2366
Nucleic Acid Atoms
Solvent Atoms170
Heterogen Atoms27

Software

Software
Software NamePurpose
StructureStudiodata collection
CNSrefinement
XDSdata reduction
XDSdata scaling
CNSphasing