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The Crystal Structure of polo-box domain of PLK1 from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6AX4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 31% PEG3350, 0.1M Bis Tris pH 5.8
Crystal Properties Matthews coefficient Solvent content 1.98 37.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.181 α = 90 b = 92.786 β = 101.642 c = 35.89 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 PILATUS3 6M 2021-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.000000 SPring-8 BL45XU
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 1.95 46.39 98.1 0.051 12.7 5.2 15223
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 1.95 2 0.328
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 FREE R-VALUE 1.95 35.176 15199 756 97.894 0.191 0.1885 0.1966 0.2448 0.2462 44.155
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] -0.258 1.802 -0.381 -0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.442 r_dihedral_angle_6_deg 15.279 r_dihedral_angle_2_deg 11.373 r_lrange_other 9.715 r_lrange_it 9.701 r_scangle_it 6.96 r_scangle_other 6.958 r_dihedral_angle_1_deg 6.837 r_mcangle_it 5.502 r_mcangle_other 5.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.442 r_dihedral_angle_6_deg 15.279 r_dihedral_angle_2_deg 11.373 r_lrange_other 9.715 r_lrange_it 9.701 r_scangle_it 6.96 r_scangle_other 6.958 r_dihedral_angle_1_deg 6.837 r_mcangle_it 5.502 r_mcangle_other 5.5 r_scbond_it 4.596 r_scbond_other 4.595 r_mcbond_it 4.024 r_mcbond_other 4.016 r_angle_refined_deg 1.423 r_angle_other_deg 0.468 r_symmetry_xyhbond_nbd_refined 0.316 r_nbd_refined 0.22 r_symmetry_nbd_refined 0.204 r_symmetry_nbd_other 0.197 r_nbd_other 0.185 r_xyhbond_nbd_refined 0.179 r_nbtor_refined 0.178 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.062 r_symmetry_xyhbond_nbd_other 0.053 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1803 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing