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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 2.38 48.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.119 α = 90 b = 109.119 β = 90 c = 136.207 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 2.108 85.161 95.6 0.216 0.999 13.7 26.8 39374
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 2.108 2.285 58.7 2.657 0.582 1.5 25.5
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 2.108 85.161 39374 1989 81.906 0.187 0.1844 0.1829 0.2347 0.2356 44.579
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] 0.005 0.005 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.356 r_dihedral_angle_6_deg 17.429 r_lrange_it 11.791 r_lrange_other 11.774 r_scangle_it 9.727 r_scangle_other 9.505 r_dihedral_angle_2_deg 7.328 r_scbond_it 7.192 r_scbond_other 7.026 r_dihedral_angle_1_deg 6.712
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.356 r_dihedral_angle_6_deg 17.429 r_lrange_it 11.791 r_lrange_other 11.774 r_scangle_it 9.727 r_scangle_other 9.505 r_dihedral_angle_2_deg 7.328 r_scbond_it 7.192 r_scbond_other 7.026 r_dihedral_angle_1_deg 6.712 r_mcangle_it 6.614 r_mcangle_other 6.614 r_mcbond_it 5.108 r_mcbond_other 5.108 r_angle_refined_deg 1.632 r_angle_other_deg 0.561 r_symmetry_nbd_refined 0.226 r_nbd_refined 0.214 r_symmetry_nbd_other 0.191 r_xyhbond_nbd_refined 0.183 r_nbd_other 0.183 r_nbtor_refined 0.163 r_symmetry_xyhbond_nbd_refined 0.155 r_chiral_restr_other 0.089 r_chiral_restr 0.081 r_symmetry_nbtor_other 0.074 r_symmetry_xyhbond_nbd_other 0.046 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5779 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing