2C6L | pdb_00002c6l

Crystal structure of the human CDK2 complexed with the triazolopyrimidine 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 DROP7.2PEG3350, HEPES PH7.2, AMMONIUM ACETATE, VAPOR DIFFUSION HANGING DROP, ROOM TEMPERATURE, pH 7.20
Crystal Properties
Matthews coefficientSolvent content
239.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.664α = 90
b = 71.806β = 90
c = 72.083γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU MSCMIRRORS2003-05-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R

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
11.93092.20.095.94.7520904
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)
11.91.9681.10.41.83.72

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1B392.3151080097491.80.1850.1760.190.2810.28RANDOM42.08
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]
0.84-1.80.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.772
r_angle_refined_deg1.389
r_chiral_restr0.257
r_nbd_refined0.211
r_symmetry_vdw_refined0.2
r_xyhbond_nbd_refined0.191
r_symmetry_hbond_refined0.174
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2340
Nucleic Acid Atoms
Solvent Atoms241
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
d*TREKdata scaling
MOLREPphasing