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Structure of the Catalytic Domain of Human Polo-like Kinase 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MQ4 PDB entry 1MQ4 (residues 274-307 deleted).
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 Protein buffer: 50 mM HEPES, pH 7.5, 5 mM TCEP. Protein was incubated on ice with 5 mM ligand (1:20 dilution of 100 mM stock in H2O for AMPPNP or DMSO for PHA-680626) for 0.5-1 h, followed by a brief centrifugation step and drop setting at RT (0.5 microliter protein + 0.5 microliter reservoir solution consisting of 500 mM magnesium acetate, 10 % PEG 4000 and 0.3 mM zinc acetate for AMPPNP, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.57 52.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.958 α = 90 b = 65.958 β = 90 c = 154.045 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 210 2006-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 45.9 0.063 23.26 5.6 14898
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 71.6 0.319 1.85 3.9 817
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 1MQ4 (residues 274-307 deleted). 2.4 45.9 14116 757 93.98 0.20463 0.20302 0.2917 0.23534 0.2994 RANDOM 22.44
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] 4.25 2.12 4.25 -6.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.08 r_scangle_it 1.823 r_angle_refined_deg 1.246 r_scbond_it 1.051 r_angle_other_deg 0.887 r_mcangle_it 0.796 r_mcbond_it 0.421 r_symmetry_hbond_refined 0.374 r_nbd_other 0.217 r_symmetry_vdw_other 0.212
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.08 r_scangle_it 1.823 r_angle_refined_deg 1.246 r_scbond_it 1.051 r_angle_other_deg 0.887 r_mcangle_it 0.796 r_mcbond_it 0.421 r_symmetry_hbond_refined 0.374 r_nbd_other 0.217 r_symmetry_vdw_other 0.212 r_nbd_refined 0.181 r_symmetry_vdw_refined 0.171 r_xyhbond_nbd_refined 0.164 r_chiral_restr 0.149 r_nbtor_other 0.082 r_metal_ion_refined 0.042 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_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 2366 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement JDirector data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing