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Crystal Structure of the Human vaccinia-related kinase bound to a phenyl-pteridinone 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 2.65 53.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.576 α = 90 b = 97.562 β = 90 c = 193.284 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 1.9 19.89 99.8 0.138 0.166 0.092 0.996 10.7 6 137864
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 1.9 1.93 99.7 1.512 1.798 0.966 0.698 1.9 6.2
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 1.9 19.89 131052 6723 99.7 0.18357 0.18197 0.1916 0.2147 0.2224 RANDOM 29.63
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 1.64 -1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.27 r_dihedral_angle_4_deg 15.131 r_dihedral_angle_3_deg 11.987 r_dihedral_angle_1_deg 6.069 r_long_range_B_refined 5.612 r_long_range_B_other 5.612 r_scangle_other 3.866 r_mcangle_it 2.971 r_mcangle_other 2.971 r_scbond_it 2.491
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.27 r_dihedral_angle_4_deg 15.131 r_dihedral_angle_3_deg 11.987 r_dihedral_angle_1_deg 6.069 r_long_range_B_refined 5.612 r_long_range_B_other 5.612 r_scangle_other 3.866 r_mcangle_it 2.971 r_mcangle_other 2.971 r_scbond_it 2.491 r_scbond_other 2.491 r_mcbond_it 2.018 r_mcbond_other 2.015 r_angle_refined_deg 1.442 r_angle_other_deg 0.95 r_chiral_restr 0.087 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 9787 Nucleic Acid Atoms Solvent Atoms 979 Heterogen Atoms 107
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing