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Crystal structure of checkpoint kinase 2 in complex with inhibitor PV1115
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CN5 PDB ENTRY 2CN5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.8 0.1M HEPES PH 7.8, 0.1M MAGNESIUM NITRATE, 14% W/V PEG 3350, 16% V/V ETHYLENE GLYCOL
Crystal Properties Matthews coefficient Solvent content 3.05 59.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.039 α = 90 b = 91.039 β = 90 c = 93.32 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH 2007-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.05 50 93.2 0.06 28.3 3.1 26596 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.1 95.9 0.4 2.6 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2CN5 2.05 50 24780 1330 91.53 0.2111 0.20915 0.2278 0.24729 0.2642 RANDOM 45.854
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 -0.24 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.155 r_dihedral_angle_4_deg 20.334 r_dihedral_angle_3_deg 15.103 r_dihedral_angle_1_deg 5.234 r_scangle_it 2.881 r_scbond_it 1.775 r_angle_refined_deg 1.324 r_mcangle_it 1.237 r_angle_other_deg 0.86 r_mcbond_it 0.669
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.155 r_dihedral_angle_4_deg 20.334 r_dihedral_angle_3_deg 15.103 r_dihedral_angle_1_deg 5.234 r_scangle_it 2.881 r_scbond_it 1.775 r_angle_refined_deg 1.324 r_mcangle_it 1.237 r_angle_other_deg 0.86 r_mcbond_it 0.669 r_mcbond_other 0.146 r_chiral_restr 0.078 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 2274 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction SCALEPACK data scaling MOLREP phasing