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Crystal structure of the cryptic polo box domain of human activated Plk4 variant 1
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, HANGING DROP 8 293 4.3M Ammonium Acetate
0.1M BisTris propane
pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.46 50.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.659 α = 90 b = 61.659 β = 90 c = 137.276 γ = 120
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 R CdTe 300K 2017-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.9793 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.64 50 99.9 49.7 11.7 17096
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.64 2.73 100 0.886 2.8 11.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4N9J 2.64 34.77 16254 838 99.86 0.23803 0.234 0.2397 0.31396 0.3018 RANDOM 82.374
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] -1.29 -0.65 -1.29 4.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.55 r_dihedral_angle_4_deg 23.643 r_dihedral_angle_3_deg 19.334 r_long_range_B_refined 11.203 r_long_range_B_other 11.201 r_dihedral_angle_1_deg 9.117 r_mcangle_it 8.742 r_mcangle_other 8.735 r_scangle_other 8.222 r_mcbond_it 6.257
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.55 r_dihedral_angle_4_deg 23.643 r_dihedral_angle_3_deg 19.334 r_long_range_B_refined 11.203 r_long_range_B_other 11.201 r_dihedral_angle_1_deg 9.117 r_mcangle_it 8.742 r_mcangle_other 8.735 r_scangle_other 8.222 r_mcbond_it 6.257 r_mcbond_other 6.253 r_scbond_it 5.94 r_scbond_other 5.939 r_angle_refined_deg 2.005 r_angle_other_deg 1.349 r_chiral_restr 0.074 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2933 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing Coot model building