2YCQ

Crystal structure of checkpoint kinase 2 in complex with inhibitor PV1115


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CN5PDB ENTRY 2CN5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.80.1M HEPES PH 7.8, 0.1M MAGNESIUM NITRATE, 14% W/V PEG 3350, 16% V/V ETHYLENE GLYCOL
Crystal Properties
Matthews coefficientSolvent content
3.0559.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.039α = 90
b = 91.039β = 90
c = 93.32γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2007-06-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BMAPS22-BM

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
12.055093.20.0628.33.1265962
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)
12.052.195.90.42.63

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 2CN52.055024780133091.530.21110.209150.24729RANDOM45.854
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]
-0.24-0.12-0.240.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.155
r_dihedral_angle_4_deg20.334
r_dihedral_angle_3_deg15.103
r_dihedral_angle_1_deg5.234
r_scangle_it2.881
r_scbond_it1.775
r_angle_refined_deg1.324
r_mcangle_it1.237
r_angle_other_deg0.86
r_mcbond_it0.669
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.155
r_dihedral_angle_4_deg20.334
r_dihedral_angle_3_deg15.103
r_dihedral_angle_1_deg5.234
r_scangle_it2.881
r_scbond_it1.775
r_angle_refined_deg1.324
r_mcangle_it1.237
r_angle_other_deg0.86
r_mcbond_it0.669
r_mcbond_other0.146
r_chiral_restr0.078
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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_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 Atoms2274
Nucleic Acid Atoms
Solvent Atoms163
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
SCALEPACKdata scaling
MOLREPphasing