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CRYSTAL STRUCTURE OF WILD-TYPE PLK1 KINASE DOMAIN IN COMPLEX WITH THIAZOLIDINONE INHIBITOR COMPOUND 1 AND A SELECTIVE DARPIN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V5Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 303 0.1 M TRIS-HCL PH 8.0, 8% PEG 5000 MME, 0.01 M EDTA SODIUM SALT AT 303 K.
Crystal Properties Matthews coefficient Solvent content 2.73 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.072 α = 90 b = 136.899 β = 90 c = 140.729 γ = 90
Symmetry Space Group P 21 21 21
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 4 2007-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 2.2 68.54 92.5 0.059 13.8 2.9 56436
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.33 90.7 0.886 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.2 68.54 53613 2826 92.42 0.19067 0.18816 0.1955 0.2385 0.242 RANDOM 61.325
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] -2.97 1.36 1.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.337 r_dihedral_angle_4_deg 17.387 r_dihedral_angle_3_deg 15.799 r_long_range_B_refined 10.927 r_long_range_B_other 10.926 r_scangle_other 8.764 r_mcangle_it 6.739 r_mcangle_other 6.739 r_dihedral_angle_1_deg 6.723 r_scbond_it 6.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.337 r_dihedral_angle_4_deg 17.387 r_dihedral_angle_3_deg 15.799 r_long_range_B_refined 10.927 r_long_range_B_other 10.926 r_scangle_other 8.764 r_mcangle_it 6.739 r_mcangle_other 6.739 r_dihedral_angle_1_deg 6.723 r_scbond_it 6.301 r_scbond_other 6.296 r_mcbond_it 4.922 r_mcbond_other 4.918 r_angle_refined_deg 1.735 r_angle_other_deg 1.318 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6650 Nucleic Acid Atoms Solvent Atoms 388 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing SCALA data scaling PDB_EXTRACT data extraction