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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 3BEO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 292 0.2 M Ammonium sulfate
50 mM BIS-TRIS pH 5.6
28% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.37 47.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.315 α = 90 b = 109.315 β = 90 c = 135.866 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 2021-11-27 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) 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 2.271 85.17 95.7 0.201 0.999 14.6 26.8 36587
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.271 2.353 52.8 3.536 0.59 1.2 27.7
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 3BEO 2.271 85.17 36587 1828 94.626 0.18 0.1772 0.1765 0.2376 0.2397 48.125
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] -0.086 -0.086 0.172
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.92 r_dihedral_angle_6_deg 17.387 r_dihedral_angle_2_deg 13.97 r_lrange_it 12.478 r_lrange_other 12.474 r_scangle_it 10.331 r_scangle_other 10.005 r_scbond_it 7.706 r_scbond_other 7.45 r_mcangle_it 7.153
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.92 r_dihedral_angle_6_deg 17.387 r_dihedral_angle_2_deg 13.97 r_lrange_it 12.478 r_lrange_other 12.474 r_scangle_it 10.331 r_scangle_other 10.005 r_scbond_it 7.706 r_scbond_other 7.45 r_mcangle_it 7.153 r_mcangle_other 7.152 r_dihedral_angle_1_deg 6.794 r_mcbond_it 5.533 r_mcbond_other 5.533 r_angle_refined_deg 1.639 r_angle_other_deg 0.559 r_nbd_refined 0.215 r_symmetry_xyhbond_nbd_refined 0.197 r_xyhbond_nbd_refined 0.193 r_symmetry_nbd_other 0.191 r_symmetry_nbd_refined 0.189 r_nbd_other 0.167 r_nbtor_refined 0.162 r_chiral_restr 0.077 r_symmetry_nbtor_other 0.073 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_symmetry_xyhbond_nbd_other 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5792 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing