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PAC FragmentDEL: Photoactivated covalent capture of DNA encoded fragments for hit discovery
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BVA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 0.8M Na/K tartrate
0.1M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.49 50.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.897 α = 90 b = 61.897 β = 90 c = 180.162 γ = 90
Symmetry Space Group P 41 21 2
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 EIGER2 XE 16M 2021-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 2.037 58.589 94.6 0.097 0.099 0.019 1 21.4 26 20091
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 2.037 2.173 52.6 2.747 2.801 0.542 0.699 1.4 26.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2BVA 2.037 58.539 20091 1017 86.065 0.188 0.1842 0.1843 0.2501 0.2504 48.888
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] -0.102 -0.102 0.204
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.338 r_dihedral_angle_6_deg 16.447 r_dihedral_angle_2_deg 15.368 r_lrange_other 9.549 r_lrange_it 9.542 r_scangle_it 7.544 r_scangle_other 7.542 r_dihedral_angle_1_deg 6.923 r_mcangle_it 5.7 r_mcangle_other 5.699
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.338 r_dihedral_angle_6_deg 16.447 r_dihedral_angle_2_deg 15.368 r_lrange_other 9.549 r_lrange_it 9.542 r_scangle_it 7.544 r_scangle_other 7.542 r_dihedral_angle_1_deg 6.923 r_mcangle_it 5.7 r_mcangle_other 5.699 r_scbond_it 5.674 r_scbond_other 5.672 r_mcbond_it 4.553 r_mcbond_other 4.55 r_angle_refined_deg 1.531 r_angle_other_deg 0.507 r_symmetry_xyhbond_nbd_refined 0.354 r_nbd_refined 0.208 r_symmetry_nbd_refined 0.206 r_symmetry_nbd_other 0.193 r_nbd_other 0.185 r_xyhbond_nbd_refined 0.184 r_nbtor_refined 0.167 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2312 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling Coot model building