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Crystal Structure of the Human vaccinia-related kinase bound to a N-propynyl-N-ethyl-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 6 293 25% PEG3350, 300 mM LiSO4, 0.1M SBG, pH 6.0, 30% glycerol
Crystal Properties Matthews coefficient Solvent content 2.62 53.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.492 α = 90 b = 96.56 β = 90 c = 193.395 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 315 2017-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.968620 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 2.15 29.67 99.9 0.181 0.223 0.128 0.99 6.5 5.3 94709
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 2.15 2.19 99.9 1.02 1.262 0.732 0.634 1.4 5.3
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 3OP5 2.15 29.67 89796 4834 99.82 0.2026 0.20065 0.2067 0.23885 0.2422 RANDOM 30.416
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] 0.12 -0.17 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.746 r_dihedral_angle_4_deg 16.866 r_dihedral_angle_3_deg 13.188 r_dihedral_angle_1_deg 6.087 r_long_range_B_refined 4.148 r_long_range_B_other 4.148 r_angle_refined_deg 1.307 r_angle_other_deg 0.948 r_mcangle_it 0.858 r_mcangle_other 0.858
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.746 r_dihedral_angle_4_deg 16.866 r_dihedral_angle_3_deg 13.188 r_dihedral_angle_1_deg 6.087 r_long_range_B_refined 4.148 r_long_range_B_other 4.148 r_angle_refined_deg 1.307 r_angle_other_deg 0.948 r_mcangle_it 0.858 r_mcangle_other 0.858 r_mcbond_it 0.457 r_mcbond_other 0.455 r_scangle_other 0.452 r_scbond_it 0.272 r_scbond_other 0.272 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 9842 Nucleic Acid Atoms Solvent Atoms 644 Heterogen Atoms 149
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing