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Crystal Structure of the Human vaccinia-related kinase bound to a N,N-dipropyl-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, 200 mM LiSO4, 0.1M SBG, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.57 52.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.596 α = 90 b = 96.168 β = 90 c = 191.871 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 0.968610 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 2.1 33.96 100 0.106 0.066 0.998 11.9 6.7 99522
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 2.1 2.14 100 1.157 0.736 0.687 1.5 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 2.1 33.96 94402 5033 99.92 0.19622 0.19463 0.2052 0.22555 0.2318 RANDOM 44.064
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] 0.07 1.55 -1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.134 r_dihedral_angle_4_deg 14.008 r_dihedral_angle_3_deg 13.76 r_dihedral_angle_1_deg 6.394 r_long_range_B_refined 3.746 r_long_range_B_other 3.746 r_scangle_other 1.609 r_angle_refined_deg 1.498 r_mcangle_it 1.476 r_mcangle_other 1.476
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.134 r_dihedral_angle_4_deg 14.008 r_dihedral_angle_3_deg 13.76 r_dihedral_angle_1_deg 6.394 r_long_range_B_refined 3.746 r_long_range_B_other 3.746 r_scangle_other 1.609 r_angle_refined_deg 1.498 r_mcangle_it 1.476 r_mcangle_other 1.476 r_scbond_it 1.03 r_scbond_other 1.029 r_angle_other_deg 0.987 r_mcbond_it 0.897 r_mcbond_other 0.881 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 9855 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 134
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing