2V0D

Crystal structure of human CDK2 complexed with a thiazolidinone inhibitor


X-RAY DIFFRACTION

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 = 53.459α = 90
b = 71.85β = 90
c = 72.011γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATERIGAKU MSCMIRRORS2003-06-16MSINGLE 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
123098.10.087.82.3189851

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONOTHERTHROUGHOUT2.281334070198.40.1970.1930.286RANDOM24.7
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]
0.23-0.680.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.368
r_dihedral_angle_4_deg21.501
r_dihedral_angle_3_deg17.774
r_dihedral_angle_1_deg7.128
r_scangle_it3.359
r_scbond_it2.303
r_angle_refined_deg1.774
r_mcangle_it1.558
r_mcbond_it0.945
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.368
r_dihedral_angle_4_deg21.501
r_dihedral_angle_3_deg17.774
r_dihedral_angle_1_deg7.128
r_scangle_it3.359
r_scbond_it2.303
r_angle_refined_deg1.774
r_mcangle_it1.558
r_mcbond_it0.945
r_nbtor_refined0.311
r_nbd_refined0.233
r_symmetry_hbond_refined0.2
r_xyhbond_nbd_refined0.197
r_symmetry_vdw_refined0.192
r_chiral_restr0.109
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 Atoms2345
Nucleic Acid Atoms
Solvent Atoms219
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling