2CCI

Crystal structure of phospho-CDK2 Cyclin A in complex with a peptide containing both the substrate and recruitment sites of CDC6


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.610-17% (V/V) PEG MONOMETHYLETHER 5000, 0.2 M AMMONIUM SULPHATE AND 0.1 M MES PH 5.0-6.5
Crystal Properties
Matthews coefficientSolvent content
2.855

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.42α = 90
b = 114.389β = 90
c = 170.709γ = 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 ID14-1ESRFID14-1

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
12.74097.60.1210.42.2396292
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)
12.72.8598.50.312.2

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 1QMZ2.794.92375971996970.2640.2610.321RANDOM37.66
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]
-1.570.51.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.457
r_dihedral_angle_4_deg17.83
r_dihedral_angle_3_deg17.13
r_dihedral_angle_1_deg5.337
r_angle_refined_deg1.146
r_scangle_it1.104
r_scbond_it0.657
r_mcangle_it0.506
r_nbtor_refined0.303
r_mcbond_it0.285
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.457
r_dihedral_angle_4_deg17.83
r_dihedral_angle_3_deg17.13
r_dihedral_angle_1_deg5.337
r_angle_refined_deg1.146
r_scangle_it1.104
r_scbond_it0.657
r_mcangle_it0.506
r_nbtor_refined0.303
r_mcbond_it0.285
r_symmetry_hbond_refined0.278
r_nbd_refined0.2
r_symmetry_vdw_refined0.179
r_xyhbond_nbd_refined0.138
r_chiral_restr0.077
r_bond_refined_d0.008
r_gen_planes_refined0.003
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 Atoms9216
Nucleic Acid Atoms
Solvent Atoms111
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing