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Crystal Structure of Human Vaccinia-related kinase 2 (VRK-2) bound to pyridin-benzenesulfonamide inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UU1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 293 27.5% PEG3350; 200 mM LiSO4; 0.1M SBG (each Sodium-tartrate + Bis-Tris + Glycylglycine) pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.15 42.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.528 α = 90 b = 67.625 β = 90 c = 171.346 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 CCD ADSC QUANTUM 315r 2017-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.979100 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.45 29.1 99.9 0.137 0.15 0.061 0.998 10.8 10.6 24095
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.55 99.9 1.773 1.96 0.824 0.707 1.2 10.3
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 THROUGHOUT 5UU1 2.45 29.1 22794 1241 99.75 0.22443 0.22061 0.2295 0.29694 0.2986 RANDOM 65.063
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] -4.63 11.7 -7.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.996 r_dihedral_angle_3_deg 14.575 r_dihedral_angle_4_deg 13.401 r_long_range_B_refined 11.299 r_long_range_B_other 11.298 r_mcangle_it 6.337 r_mcangle_other 6.336 r_scangle_other 6.086 r_dihedral_angle_1_deg 5.043 r_mcbond_it 3.925
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.996 r_dihedral_angle_3_deg 14.575 r_dihedral_angle_4_deg 13.401 r_long_range_B_refined 11.299 r_long_range_B_other 11.298 r_mcangle_it 6.337 r_mcangle_other 6.336 r_scangle_other 6.086 r_dihedral_angle_1_deg 5.043 r_mcbond_it 3.925 r_mcbond_other 3.925 r_scbond_it 3.8 r_scbond_other 3.8 r_angle_refined_deg 1.199 r_angle_other_deg 0.779 r_chiral_restr 0.062 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 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 4466 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing