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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
Crystal Properties Matthews coefficient Solvent content 2.69 54.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.605 α = 90 b = 135.302 β = 90 c = 136.7 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 315 2006-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.037 ESRF ID29
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 2.24 96.16 97.9 0.084 14.6 4.2 233157 40.5
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 2.24 2.38 90.7 1.118 1.2 3.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.243 48.128 55347 2826 98.06 0.191 0.1882 0.1928 0.236 0.2351 50.407
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] 0.604 -0.436 -0.168
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.088 r_dihedral_angle_3_deg 12.776 r_lrange_other 10.339 r_lrange_it 10.332 r_scangle_it 8.471 r_scangle_other 8.47 r_dihedral_angle_2_deg 7.278 r_mcangle_other 6.802 r_mcangle_it 6.796 r_dihedral_angle_1_deg 6.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.088 r_dihedral_angle_3_deg 12.776 r_lrange_other 10.339 r_lrange_it 10.332 r_scangle_it 8.471 r_scangle_other 8.47 r_dihedral_angle_2_deg 7.278 r_mcangle_other 6.802 r_mcangle_it 6.796 r_dihedral_angle_1_deg 6.41 r_scbond_it 6.044 r_scbond_other 6.044 r_mcbond_it 4.876 r_mcbond_other 4.876 r_angle_refined_deg 1.352 r_angle_other_deg 0.505 r_symmetry_nbd_refined 0.296 r_nbd_refined 0.215 r_symmetry_xyhbond_nbd_refined 0.213 r_symmetry_nbd_other 0.191 r_nbd_other 0.185 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.148 r_ncsr_local_group_1 0.125 r_ncsr_local_group_2 0.093 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.069 r_chiral_restr_other 0.032 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6620 Nucleic Acid Atoms Solvent Atoms 329 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing