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The Crystal Structure of PLK1 from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OWB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.5M MgAc2, 12% PEG 4000, 0.3mM ZnAc2
Crystal Properties Matthews coefficient Solvent content 2.69 54.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.5 α = 90 b = 67.5 β = 90 c = 153.347 γ = 120
Symmetry Space Group P 32 2 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 EIGER X 16M 2023-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95365 Australian Synchrotron MX2
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 2.2 46.53 96.2 0.111 12.5 11 20455
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) 1 2.2 2.27 1.003
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.2 46.53 20408 963 95.947 0.198 0.195 0.2497 0.2325 46.856
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] 1.53 0.765 1.53 -4.964
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.842 r_dihedral_angle_3_deg 13.55 r_dihedral_angle_4_deg 12.73 r_dihedral_angle_1_deg 6.519 r_lrange_it 6.036 r_lrange_other 6.015 r_scangle_it 4.081 r_scangle_other 4.08 r_mcangle_it 3.45 r_mcangle_other 3.449
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.842 r_dihedral_angle_3_deg 13.55 r_dihedral_angle_4_deg 12.73 r_dihedral_angle_1_deg 6.519 r_lrange_it 6.036 r_lrange_other 6.015 r_scangle_it 4.081 r_scangle_other 4.08 r_mcangle_it 3.45 r_mcangle_other 3.449 r_scbond_it 2.458 r_scbond_other 2.458 r_mcbond_it 2.146 r_mcbond_other 2.142 r_angle_refined_deg 1.241 r_angle_other_deg 1.099 r_symmetry_nbd_refined 0.265 r_nbd_other 0.209 r_nbd_refined 0.188 r_symmetry_nbd_other 0.165 r_nbtor_refined 0.157 r_chiral_restr_other 0.129 r_xyhbond_nbd_refined 0.126 r_symmetry_xyhbond_nbd_refined 0.087 r_symmetry_nbtor_other 0.071 r_chiral_restr 0.052 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2379 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing