3DDQ | pdb_00003ddq

Structure of phosphorylated Thr160 CDK2/cyclin A in complex with the inhibitor roscovitine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7277ammonium sulphate, potassium chloride, Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.8156.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.421α = 90
b = 133.376β = 90
c = 147.509γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42006-02-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.82090.20.0716.412269222
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)
1.81.984.10.2853.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.8202117586117586494789.980.195970.1950.194620.19370.228890.2272RANDOM22.179
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]
0.050.24-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.495
r_dihedral_angle_4_deg14.466
r_dihedral_angle_3_deg13.839
r_dihedral_angle_1_deg5.419
r_rigid_bond_restr3.106
r_scbond_it2.704
r_sphericity_free2.565
r_scangle_it2.551
r_sphericity_bonded1.924
r_angle_refined_deg1.185
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.495
r_dihedral_angle_4_deg14.466
r_dihedral_angle_3_deg13.839
r_dihedral_angle_1_deg5.419
r_rigid_bond_restr3.106
r_scbond_it2.704
r_sphericity_free2.565
r_scangle_it2.551
r_sphericity_bonded1.924
r_angle_refined_deg1.185
r_mcangle_it1.141
r_mcbond_it0.699
r_nbtor_refined0.303
r_nbd_refined0.193
r_symmetry_vdw_refined0.173
r_xyhbond_nbd_refined0.158
r_symmetry_hbond_refined0.151
r_chiral_restr0.099
r_bond_refined_d0.008
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8907
Nucleic Acid Atoms
Solvent Atoms841
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing