2UZO

Crystal structure of human CDK2 complexed with a thiazolidinone inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1B39PDB ENTRY 1B39

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7VAPOR DIFFUSION HANGING DROP, ROOM TEMPERATURE, PEG3350, HEPES PH7.2, AMMONIUM ACETATE, pH 7.00
Crystal Properties
Matthews coefficientSolvent content
2.140

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.422α = 90
b = 72.256β = 90
c = 72.33γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2003-06-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
12.22094.60.0910.24.214029

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 1B392.312115745981000.2150.2120.291RANDOM30.27
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]
0.1-0.05-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.305
r_dihedral_angle_3_deg19.395
r_dihedral_angle_4_deg18.767
r_dihedral_angle_1_deg6.614
r_scangle_it3.734
r_scbond_it2.56
r_mcangle_it1.825
r_angle_refined_deg1.776
r_mcbond_it1.101
r_symmetry_hbond_refined0.328
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.305
r_dihedral_angle_3_deg19.395
r_dihedral_angle_4_deg18.767
r_dihedral_angle_1_deg6.614
r_scangle_it3.734
r_scbond_it2.56
r_mcangle_it1.825
r_angle_refined_deg1.776
r_mcbond_it1.101
r_symmetry_hbond_refined0.328
r_nbtor_refined0.316
r_nbd_refined0.227
r_symmetry_vdw_refined0.227
r_xyhbond_nbd_refined0.2
r_chiral_restr0.133
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2321
Nucleic Acid Atoms
Solvent Atoms71
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing