2C6K

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
239.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.55α = 90
b = 71.633β = 90
c = 72.262γ = 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
11.93098.70.0611.14.4522289
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)
11.91.9788.60.312.53.72

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1B391.91520337185898.60.1890.1830.254RANDOM29.94
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]
0.86-0.85-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.863
r_scangle_it3.438
r_scbond_it2.228
r_mcangle_it1.59
r_angle_refined_deg1.488
r_mcbond_it0.884
r_chiral_restr0.262
r_nbd_refined0.219
r_symmetry_hbond_refined0.192
r_xyhbond_nbd_refined0.183
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.863
r_scangle_it3.438
r_scbond_it2.228
r_mcangle_it1.59
r_angle_refined_deg1.488
r_mcbond_it0.884
r_chiral_restr0.262
r_nbd_refined0.219
r_symmetry_hbond_refined0.192
r_xyhbond_nbd_refined0.183
r_symmetry_vdw_refined0.174
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
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 Atoms2345
Nucleic Acid Atoms
Solvent Atoms305
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
d*TREKdata scaling
MOLREPphasing