2VV9

CDK2 in complex with an imidazole piperazine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.58% PEG 3350, 0.1M HEPES PH 7.5, 0.05M AMMONIUM ACETATE
Crystal Properties
Matthews coefficientSolvent content
239

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.252α = 90
b = 71.153β = 90
c = 71.933γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM-42004-03-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.2SRSPX14.2

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
11.927.5297.30.0416.052.67214563.7
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)
11.91.9288.30.321.82.16

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 REPLACEMENTTHROUGHOUTIN-HOUSE CDK2 STRUCTURE1.927.5219641106393.50.1910.1890.228RANDOM22.15
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]
-0.352.17-1.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.585
r_scangle_it3.108
r_scbond_it1.894
r_angle_refined_deg1.501
r_angle_other_deg1.465
r_mcangle_it1.266
r_mcbond_it0.694
r_symmetry_vdw_other0.322
r_nbd_other0.253
r_nbd_refined0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.585
r_scangle_it3.108
r_scbond_it1.894
r_angle_refined_deg1.501
r_angle_other_deg1.465
r_mcangle_it1.266
r_mcbond_it0.694
r_symmetry_vdw_other0.322
r_nbd_other0.253
r_nbd_refined0.23
r_symmetry_hbond_refined0.167
r_xyhbond_nbd_refined0.159
r_symmetry_vdw_refined0.123
r_nbtor_other0.093
r_chiral_restr0.082
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_gen_planes_other0.003
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
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 Atoms2182
Nucleic Acid Atoms
Solvent Atoms152
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
TRUNCATEdata scaling
AMoREphasing