2YIT

Structural analysis of checkpoint kinase 2 in complex with PV1162, a novel inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2W0JPDB ENTRY 2W0J

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.60.1M HEPES PH 7.8, 0.2M MAGNESIUM NITRATE, 14%W/V PEG3350, 16%V/V ETHYLENE GLYCOL
Crystal Properties
Matthews coefficientSolvent content
360

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.208α = 90
b = 91.208β = 90
c = 93.465γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH MX-3002007-10-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-IDAPS22-ID

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
12.25099.70.0735.16.9233462
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)
12.22.281000.553.76.9

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 2W0J2.25022111120099.640.196360.194810.22579RANDOM46.273
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]
0.080.040.08-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.651
r_dihedral_angle_4_deg20.748
r_dihedral_angle_3_deg14.752
r_dihedral_angle_1_deg5.169
r_scangle_it3.249
r_scbond_it1.961
r_angle_refined_deg1.318
r_mcangle_it1.315
r_angle_other_deg0.846
r_mcbond_it0.694
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.651
r_dihedral_angle_4_deg20.748
r_dihedral_angle_3_deg14.752
r_dihedral_angle_1_deg5.169
r_scangle_it3.249
r_scbond_it1.961
r_angle_refined_deg1.318
r_mcangle_it1.315
r_angle_other_deg0.846
r_mcbond_it0.694
r_mcbond_other0.137
r_chiral_restr0.072
r_bond_refined_d0.013
r_gen_planes_refined0.006
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 Atoms2288
Nucleic Acid Atoms
Solvent Atoms138
Heterogen Atoms33

Software

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