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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 2.43 48.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.822 α = 90 b = 61.822 β = 90 c = 180.79 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 1.885 58.496 95.3 0.09 0.092 0.018 1 22.7 26.4 27812
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 1.885 1.952 50.6 3.058 3.115 0.588 0.638 1 27.2
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 (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 1.885 58.496 27811 1387 94.908 0.181 0.1785 0.1773 0.2265 0.2256 38.439
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] -0.051 -0.051 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.742 r_dihedral_angle_6_deg 16.412 r_lrange_it 7.424 r_lrange_other 7.387 r_dihedral_angle_1_deg 7.183 r_dihedral_angle_2_deg 6.122 r_scangle_it 5.92 r_scangle_other 5.919 r_scbond_it 4.244 r_scbond_other 4.242
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.742 r_dihedral_angle_6_deg 16.412 r_lrange_it 7.424 r_lrange_other 7.387 r_dihedral_angle_1_deg 7.183 r_dihedral_angle_2_deg 6.122 r_scangle_it 5.92 r_scangle_other 5.919 r_scbond_it 4.244 r_scbond_other 4.242 r_mcangle_it 4.159 r_mcangle_other 4.159 r_mcbond_it 3.397 r_mcbond_other 3.394 r_angle_refined_deg 1.539 r_angle_other_deg 0.524 r_symmetry_xyhbond_nbd_refined 0.279 r_nbd_refined 0.213 r_nbd_other 0.21 r_xyhbond_nbd_refined 0.204 r_symmetry_nbd_refined 0.204 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.17 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.078 r_symmetry_xyhbond_nbd_other 0.048 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2308 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling Coot model building