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Structure of Human Vaccinia-related Kinase 1 (VRK1) Bound to ACH000400
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UVF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 22% PEG3350, 20 mM Li2SO4, 0.1 M Buffer system SBG pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.56 52.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.552 α = 90 b = 96.615 β = 90 c = 190.858 γ = 90
Symmetry Space Group P 21 21 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 2021-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
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 2.3 19.93 99.7 0.176 11.8 13.6 75682
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 2.3 2.35 99.6 2.417 1.8 13.8
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.3 19.93 75597 3800 99.6 0.199 0.2025 0.231 0.2328 RANDOM 53.97
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] 1.304 0.523 -1.827
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.942 r_dihedral_angle_2_deg 7.314 r_dihedral_angle_1_deg 5.641 r_scangle_it 3.035 r_scangle_other 3.035 r_mcangle_it 2.537 r_mcangle_other 2.537 r_scbond_it 1.773 r_scbond_other 1.773 r_mcbond_it 1.499
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.942 r_dihedral_angle_2_deg 7.314 r_dihedral_angle_1_deg 5.641 r_scangle_it 3.035 r_scangle_other 3.035 r_mcangle_it 2.537 r_mcangle_other 2.537 r_scbond_it 1.773 r_scbond_other 1.773 r_mcbond_it 1.499 r_mcbond_other 1.499 r_angle_refined_deg 0.916 r_angle_other_deg 0.361 r_nbd_refined 0.19 r_nbtor_refined 0.178 r_nbd_other 0.157 r_xyhbond_nbd_refined 0.116 r_chiral_restr 0.047 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbtor_other 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_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9661 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing