2CCH

The crystal structure of CDK2 cyclin A in complex with a substrate peptide derived from CDC modified with a gamma-linked ATP analogue


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QMZPDB ENTRY 1QMZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.627713% PEG MONOMETHYLETHER 5000, 0.2 M AMMONIUM SULPHATE, 0.1 M CITRATE/ACETATE BUFFER PH 5.6 AT 4 C
Crystal Properties
Matthews coefficientSolvent content
2.957.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.535α = 90
b = 114.483β = 90
c = 181.299γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2005-11-12MSINGLE 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
11.796980.0615.13.61677022
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)
11.71.7991.50.372.8

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 1QMZ1.796.67159215841098.20.150.1480.182RANDOM20.79
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]
0.32-1.230.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.078
r_dihedral_angle_4_deg17.764
r_dihedral_angle_3_deg13.909
r_dihedral_angle_1_deg5.701
r_scangle_it3.895
r_scbond_it2.957
r_mcangle_it1.983
r_mcbond_it1.674
r_angle_refined_deg1.59
r_angle_other_deg0.894
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.078
r_dihedral_angle_4_deg17.764
r_dihedral_angle_3_deg13.909
r_dihedral_angle_1_deg5.701
r_scangle_it3.895
r_scbond_it2.957
r_mcangle_it1.983
r_mcbond_it1.674
r_angle_refined_deg1.59
r_angle_other_deg0.894
r_symmetry_hbond_refined0.364
r_symmetry_vdw_refined0.356
r_symmetry_vdw_other0.345
r_nbd_refined0.233
r_xyhbond_nbd_refined0.199
r_nbd_other0.194
r_nbtor_refined0.18
r_chiral_restr0.149
r_nbtor_other0.086
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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 Atoms9148
Nucleic Acid Atoms
Solvent Atoms1045
Heterogen Atoms79

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing