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The Crystal Structure of polo box domain of Plk4 from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4N9J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 2.00M Ammonium sulfate, 100mM TRIS, pH7.0, 200mM Lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.76 55.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.304 α = 90 b = 77.614 β = 90 c = 120.644 γ = 90
Symmetry Space Group P 21 2 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 PIXEL DECTRIS PILATUS 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 2.7 48.59 100 0.106 15.1 9.1 16692
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 2.7 2.83 1.031
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 2.7 48 16663 861 99.922 0.211 0.2086 0.2124 0.2603 0.2614 63.247
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] -1.477 1.442 0.034
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.228 r_dihedral_angle_3_deg 12.047 r_lrange_it 8.975 r_lrange_other 8.965 r_dihedral_angle_1_deg 6.845 r_scangle_it 5.313 r_scangle_other 5.292 r_mcangle_it 5.277 r_mcangle_other 5.276 r_dihedral_angle_2_deg 4.479
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.228 r_dihedral_angle_3_deg 12.047 r_lrange_it 8.975 r_lrange_other 8.965 r_dihedral_angle_1_deg 6.845 r_scangle_it 5.313 r_scangle_other 5.292 r_mcangle_it 5.277 r_mcangle_other 5.276 r_dihedral_angle_2_deg 4.479 r_mcbond_it 3.193 r_mcbond_other 3.193 r_scbond_it 3.171 r_scbond_other 3.136 r_angle_refined_deg 0.874 r_angle_other_deg 0.296 r_nbd_refined 0.191 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.174 r_symmetry_xyhbond_nbd_refined 0.172 r_xyhbond_nbd_refined 0.151 r_nbd_other 0.128 r_symmetry_nbd_refined 0.121 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.038 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3639 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing