4FKL

Crystal structure of the cdk2 in complex with thiazolylpyrimidine inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2R3IPDB ENTRY 2R3I

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.8293.1515-20% PEG3350, 0.2M AMMONIUM ACETATE, 0.1M HEPES, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K, pH 7.8
Crystal Properties
Matthews coefficientSolvent content
2.0339.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.333α = 90
b = 71.532β = 90
c = 72.486γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDMIRRORS2009-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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
11.265099.90.06217.113.97564975574-3
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)
11.261.2899.90.25911.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2R3I1.2622.8975492380599.90.1530.1510.183RANDOM17.81
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]
-0.040.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.468
r_dihedral_angle_4_deg19.069
r_dihedral_angle_3_deg13.275
r_scangle_it5.423
r_dihedral_angle_1_deg5.259
r_scbond_it3.814
r_mcangle_it3.162
r_mcbond_it2.045
r_rigid_bond_restr1.9
r_angle_refined_deg1.736
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.468
r_dihedral_angle_4_deg19.069
r_dihedral_angle_3_deg13.275
r_scangle_it5.423
r_dihedral_angle_1_deg5.259
r_scbond_it3.814
r_mcangle_it3.162
r_mcbond_it2.045
r_rigid_bond_restr1.9
r_angle_refined_deg1.736
r_chiral_restr0.115
r_bond_refined_d0.016
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2339
Nucleic Acid Atoms
Solvent Atoms247
Heterogen Atoms14

Software

Software
Software NamePurpose
MD2data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling