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Crystal structure of an activated (Thr->Asp) Polo-like kinase 1 (Plk1) catalytic domain.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MQ4
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 7 mg/ml in 50 mM Tris-HCl pH 7.5, 200 mM NaCl and 3 mM DTT; crystallization condition: 0.1 M HEPES pH 7.5, 0.2 M (NH4)2SO4, 25% PEG 3350, and 5% glycerol; cryoprotectant: 15% ethylene glycol., VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.83 56.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.767 α = 90 b = 134.767 β = 90 c = 134.767 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 ADSC QUANTUM 315 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 2.4 30 99.7 0.057 9.8 5.4 16020
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) 2.4 2.53 100 0.376 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 1mq4 2.4 30 14785 1227 99.63 0.23665 0.23396 0.2326 0.26897 0.2677 RANDOM 53.555
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 29.487 r_dihedral_angle_4_deg 13.88 r_dihedral_angle_3_deg 13.736 r_dihedral_angle_1_deg 4.169 r_mcangle_it 2.372 r_scangle_it 1.778 r_mcbond_it 1.357 r_scbond_it 1.038 r_angle_refined_deg 0.866 r_nbtor_refined 0.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.487 r_dihedral_angle_4_deg 13.88 r_dihedral_angle_3_deg 13.736 r_dihedral_angle_1_deg 4.169 r_mcangle_it 2.372 r_scangle_it 1.778 r_mcbond_it 1.357 r_scbond_it 1.038 r_angle_refined_deg 0.866 r_nbtor_refined 0.294 r_nbd_refined 0.161 r_symmetry_vdw_refined 0.116 r_xyhbond_nbd_refined 0.092 r_symmetry_hbond_refined 0.075 r_chiral_restr 0.059 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 2091 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection CrystalClear data reduction d*TREK data scaling MOLREP phasing