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Crystal Structure of the Human vaccinia-related kinase bound to a N,N-dipropynyl-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 6.5 293 30.25% PEG3350, 200 mM LiSO4, 0.1M SBG buffer pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.58 52.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.058 α = 90 b = 95.753 β = 90 c = 192.833 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) 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 2.1 29.79 99.9 0.12 0.142 0.075 0.998 10.9 6.7 100045
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 2.1 2.14 100 1.118 1.344 0.711 0.691 1.5 6.6
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 29.79 94907 5052 99.9 0.19191 0.19029 0.2008 0.22201 0.2268 RANDOM 39.019
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] 0.71 0.32 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.822 r_dihedral_angle_4_deg 16.941 r_dihedral_angle_3_deg 13.634 r_dihedral_angle_1_deg 6.169 r_long_range_B_refined 4.497 r_long_range_B_other 4.497 r_angle_refined_deg 1.454 r_scangle_other 1.063 r_angle_other_deg 0.967 r_mcangle_it 0.954
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.822 r_dihedral_angle_4_deg 16.941 r_dihedral_angle_3_deg 13.634 r_dihedral_angle_1_deg 6.169 r_long_range_B_refined 4.497 r_long_range_B_other 4.497 r_angle_refined_deg 1.454 r_scangle_other 1.063 r_angle_other_deg 0.967 r_mcangle_it 0.954 r_mcangle_other 0.954 r_scbond_it 0.715 r_scbond_other 0.715 r_mcbond_it 0.562 r_mcbond_other 0.547 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 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 9901 Nucleic Acid Atoms Solvent Atoms 474 Heterogen Atoms 125
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing