4EZ7

CDK2 in complex with staurosporine and 2 molecules of 8-anilino-1-naphthalene sulfonic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3PXFPDB ENTRY 3PXF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52915 mg/mL CDK2 protein, 50 mM sodium/potassium phosphate, pH 7.5, 50 mM HEPES, pH 7.5, 5% v/v PEG3350, 1 mM staurosporine overnight soak followed by 20 mM ANS soak (50 mM HEPES, 50 mM phosphate, 15% v/v PEG3350, 25% v/v glycerol), VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
1.9336.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.239α = 90
b = 70.175β = 90
c = 71.781γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDRIGAKU SATURN 944+2012-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.492097.20.06647.46.9988698863
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.492.54900.3046.73.6

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 3PXF2.4919.7681.34954437096.870.22020.274RANDOM
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]
8.041322.6992.9501
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.272
f_angle_d1.087
f_chiral_restr0.07
f_bond_d0.007
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2431
Nucleic Acid Atoms
Solvent Atoms40
Heterogen Atoms93

Software

Software
Software NamePurpose
StructureStudiodata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing