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Crystal structure of a phosphorylated Polo-like kinase 1 (Plk1) catalytic domain in complex with ADP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D5V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 hanging-drop vapor diffusion at 4 C (277K); protein at 6 mg/ml in 50 mM Tris-HCl pH 7.5, 200 mM NaCl, 3 mM DTT, 4 mM ATP, and 4 mM MgSO4; crystallization condition: 0.2 M disodium tartrate dihydrate and 20% PEG 3350; cryoprotectant: 15% ethylene glycol, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.79 55.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.99 α = 90 b = 133.99 β = 90 c = 133.99 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 180 CCD MARMOSAIC 325 mm CCD 2006-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.98 SSRL BL11-1
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 2.6 30 99.9 0.053 9 6 12461
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) 2.6 2.74 99.9 0.348 2.2
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 3d5v 2.6 30 11348 1113 99.89 0.24418 0.24155 0.2303 0.2711 0.2552 RANDOM 61.518
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.795 r_dihedral_angle_3_deg 15.017 r_dihedral_angle_4_deg 14.889 r_dihedral_angle_1_deg 3.954 r_mcangle_it 2.098 r_scangle_it 1.446 r_mcbond_it 1.187 r_angle_refined_deg 0.927 r_scbond_it 0.875 r_nbtor_refined 0.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.795 r_dihedral_angle_3_deg 15.017 r_dihedral_angle_4_deg 14.889 r_dihedral_angle_1_deg 3.954 r_mcangle_it 2.098 r_scangle_it 1.446 r_mcbond_it 1.187 r_angle_refined_deg 0.927 r_scbond_it 0.875 r_nbtor_refined 0.293 r_symmetry_vdw_refined 0.167 r_nbd_refined 0.162 r_xyhbond_nbd_refined 0.099 r_symmetry_hbond_refined 0.097 r_chiral_restr 0.058 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 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_refined 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 2264 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection CrystalClear data reduction d*TREK data scaling MOLREP phasing