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Crystal Structure of the Human vaccinia-related kinase 1 bound to (R)-2-phenylaminopteridinone 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 2.58 52.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.222 α = 90 b = 95.118 β = 90 c = 193.553 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) 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 19.81 99.2 0.126 0.051 0.999 13 13.7 133129
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 1.9 1.93 98.6 1.982 0.813 0.56 13
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 19.81 126641 6431 98.97 0.1886 0.1867 0.1962 0.22589 0.2326 RANDOM 37.609
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] -0.05 2.39 -2.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.305 r_dihedral_angle_4_deg 16.066 r_dihedral_angle_3_deg 12.251 r_long_range_B_refined 6.124 r_long_range_B_other 6.123 r_dihedral_angle_1_deg 5.899 r_scangle_other 3.758 r_mcangle_it 3.063 r_mcangle_other 3.063 r_scbond_it 2.414
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.305 r_dihedral_angle_4_deg 16.066 r_dihedral_angle_3_deg 12.251 r_long_range_B_refined 6.124 r_long_range_B_other 6.123 r_dihedral_angle_1_deg 5.899 r_scangle_other 3.758 r_mcangle_it 3.063 r_mcangle_other 3.063 r_scbond_it 2.414 r_scbond_other 2.414 r_mcbond_it 2.052 r_mcbond_other 2.051 r_angle_refined_deg 1.305 r_angle_other_deg 0.933 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 9812 Nucleic Acid Atoms Solvent Atoms 1007 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing