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Crystal Structure of the Human vaccinia-related kinase bound to a N-methyl-N-propyl-dihydropteridine 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 7 293 27.5% PEG3350; 300 mM LiSO4; 0.1M SBG pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.59 52.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.83 α = 90 b = 96.987 β = 90 c = 191.67 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 2017-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96861 Diamond I24
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 2.25 34.8 100 0.192 0.226 0.119 0.993 8.3 6.7 81966
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 2.25 2.29 99.9 1.108 1.321 0.711 0.683 1.7 6.5
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 2.25 34.8 77901 3987 99.95 0.18977 0.18757 0.1952 0.23289 0.2369 RANDOM 35.987
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] -0.39 1.78 -1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.946 r_dihedral_angle_4_deg 15.12 r_dihedral_angle_3_deg 13.937 r_dihedral_angle_1_deg 6.051 r_long_range_B_refined 4.739 r_long_range_B_other 4.738 r_angle_refined_deg 1.231 r_mcangle_it 1.116 r_mcangle_other 1.116 r_scangle_other 0.948
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.946 r_dihedral_angle_4_deg 15.12 r_dihedral_angle_3_deg 13.937 r_dihedral_angle_1_deg 6.051 r_long_range_B_refined 4.739 r_long_range_B_other 4.738 r_angle_refined_deg 1.231 r_mcangle_it 1.116 r_mcangle_other 1.116 r_scangle_other 0.948 r_angle_other_deg 0.775 r_mcbond_it 0.605 r_mcbond_other 0.605 r_scbond_it 0.597 r_scbond_other 0.597 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 9905 Nucleic Acid Atoms Solvent Atoms 534 Heterogen Atoms 250
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing