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Crystal Structure of the Human vaccinia-related kinase bound to a bis-difluorophenol-aminopyridine 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 22% PEG3350; 0.02M Lithium Sulfate; 0.1M Buffer system SBG pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.99 58.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.215 α = 90 b = 96.572 β = 90 c = 193.056 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 2017-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979180 APS 24-ID-E
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 1.8 19.98 99.9 0.129 0.139 0.052 0.999 13.9 13.6 159713
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 1.8 1.83 100 2.177 2.349 0.882 0.698 1.5 13.6
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 1.8 19.98 151521 8093 99.9 0.18551 0.18403 0.193 0.2125 0.2185 RANDOM 33.218
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] -0.17 2.34 -2.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.677 r_dihedral_angle_4_deg 15.433 r_dihedral_angle_3_deg 11.92 r_long_range_B_refined 6.315 r_long_range_B_other 6.155 r_dihedral_angle_1_deg 5.843 r_scangle_other 4.372 r_mcangle_other 3.487 r_mcangle_it 3.486 r_scbond_it 2.859
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.677 r_dihedral_angle_4_deg 15.433 r_dihedral_angle_3_deg 11.92 r_long_range_B_refined 6.315 r_long_range_B_other 6.155 r_dihedral_angle_1_deg 5.843 r_scangle_other 4.372 r_mcangle_other 3.487 r_mcangle_it 3.486 r_scbond_it 2.859 r_scbond_other 2.859 r_mcbond_it 2.384 r_mcbond_other 2.382 r_angle_refined_deg 1.497 r_angle_other_deg 0.968 r_chiral_restr 0.092 r_bond_refined_d 0.012 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 9904 Nucleic Acid Atoms Solvent Atoms 1173 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing