5JQ5

Crystal structure of CDK2 in complex with inhibitor ICEC0942


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NS9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.82770.1M AMMONIUM ACETATE, PH 7.8, 6% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.0239.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.65α = 90
b = 70.77β = 90
c = 72.27γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2011-02-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54187

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
11.9450.5696.30.027213.220059
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)
11.942.0588.30.0749.22.8

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 REPLACEMENTTHROUGHOUT3NS91.9450.5619012101895.870.184160.181080.24104RANDOM19.233
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]
-0.250.29-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.867
r_dihedral_angle_4_deg17.541
r_dihedral_angle_3_deg16.588
r_dihedral_angle_1_deg5.978
r_scangle_it4.918
r_scbond_it3.13
r_mcangle_it2.084
r_angle_refined_deg2.013
r_mcbond_it1.221
r_chiral_restr0.155
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.867
r_dihedral_angle_4_deg17.541
r_dihedral_angle_3_deg16.588
r_dihedral_angle_1_deg5.978
r_scangle_it4.918
r_scbond_it3.13
r_mcangle_it2.084
r_angle_refined_deg2.013
r_mcbond_it1.221
r_chiral_restr0.155
r_bond_refined_d0.023
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms2309
Nucleic Acid Atoms
Solvent Atoms152
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing