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Crystal Structure of the Human vaccinia-related kinase 1 (VRK1) bound to an N-propynyl-N-isopentyl-dihydropteridin inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OP5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 30.25% PEG3350, 30mM LiSO4, 0.1M SBG (Sodium-tartrate, Bis-Tris, Glycylglycine)
Crystal Properties Matthews coefficient Solvent content 2.81 56.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.47 α = 90 b = 96.821 β = 90 c = 192.831 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 PILATUS3 6M 2017-12-19 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) 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 20 99.8 0.136 0.073 0.993 10.2 5.1 117261
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 100 1.001 0.565 0.585 1.6 5.1
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 3OP5 2 20 111512 5665 99.79 0.18825 0.18707 0.1963 0.21112 0.218 RANDOM 31.898
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] -0.32 0.52 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.163 r_dihedral_angle_4_deg 17.049 r_dihedral_angle_3_deg 12.683 r_dihedral_angle_1_deg 6.165 r_long_range_B_refined 5.08 r_long_range_B_other 5.08 r_angle_refined_deg 1.549 r_scangle_other 1.536 r_mcangle_it 1.409 r_mcangle_other 1.409
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.163 r_dihedral_angle_4_deg 17.049 r_dihedral_angle_3_deg 12.683 r_dihedral_angle_1_deg 6.165 r_long_range_B_refined 5.08 r_long_range_B_other 5.08 r_angle_refined_deg 1.549 r_scangle_other 1.536 r_mcangle_it 1.409 r_mcangle_other 1.409 r_angle_other_deg 0.987 r_scbond_it 0.944 r_scbond_other 0.943 r_mcbond_it 0.853 r_mcbond_other 0.814 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 9866 Nucleic Acid Atoms Solvent Atoms 816 Heterogen Atoms 202
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing