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Crystal structure of human PLK1 Polo-Box Domain in complex with Mis18
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FVH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.09 M Halogen mix (NaF, NaBr, NaI), 0.1 M buffer
system 2 (Sodium HEPES and MOPS) (pH7.5), 37% precipitant mix
MPD_P1K_P3350 (MPD (racemic), PEG 1K, PEG 3350)
Crystal Properties Matthews coefficient Solvent content 1.89 35.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.138 α = 90 b = 56.568 β = 115.74 c = 49.576 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS EIGER2 XE 16M 2021-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979499 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.94 44.66 94.6 0.978 7.16 3.2 15410 31.66
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 2.009 0.8879 0.271
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.94 44.66 1.33 15177 740 94.02 0.2194 0.2169 0.2171 0.2707 0.2739 35.5
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 f_dihedral_angle_d 7.5602 f_angle_d 1.0972 f_chiral_restr 0.0575 f_plane_restr 0.0111 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1748 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction xia2 data scaling PHASER phasing