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Crystal structure of Polo-like kinase 1 in complex with a pyrazoloquinazoline inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other In-house available PLK1 crystal structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 1.2M Na/K tartrate, 25mM Zn acetate, 0.1M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.83 56.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.352 α = 90 b = 67.352 β = 90 c = 154.109 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 ADSC QUANTUM 315r 2007-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 1.071568 ESRF ID14-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.5 58.328 99.9 0.121 0.121 12.3 5.2 14659
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.64 100 0.583 0.583 1.3 5.4 2071
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 In-house available PLK1 crystal structure 2.5 58.32 14616 736 99.9 0.21211 0.20769 0.2049 0.30317 0.2938 RANDOM 30.807
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] 1.7 0.85 1.7 -2.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.736 r_dihedral_angle_4_deg 17.489 r_dihedral_angle_3_deg 17.444 r_dihedral_angle_1_deg 6.363 r_scangle_it 2.771 r_scbond_it 1.812 r_angle_refined_deg 1.657 r_mcangle_it 1.173 r_mcbond_it 0.678 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.736 r_dihedral_angle_4_deg 17.489 r_dihedral_angle_3_deg 17.444 r_dihedral_angle_1_deg 6.363 r_scangle_it 2.771 r_scbond_it 1.812 r_angle_refined_deg 1.657 r_mcangle_it 1.173 r_mcbond_it 0.678 r_nbtor_refined 0.32 r_symmetry_vdw_refined 0.254 r_nbd_refined 0.234 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.118 r_symmetry_hbond_refined 0.113 r_metal_ion_refined 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2353 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 44
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction DNA data collection