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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 2.52 50.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.913 α = 90 b = 61.913 β = 90 c = 181.903 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 Bruker PHOTON III 2022-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER X8 PROTEUM 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.69 25.603 99.2 0.2074 10.07 14.25 18685
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.69 2.73 100 0.5548 3.45 14.25
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 2.69 25.603 10410 515 99.237 0.16 0.1552 0.154 0.2489 0.2447 29.915
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] -1.154 -1.154 2.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.498 r_dihedral_angle_2_deg 18.48 r_dihedral_angle_6_deg 15.519 r_lrange_it 9.027 r_lrange_other 9.023 r_dihedral_angle_1_deg 8.041 r_scangle_it 5.994 r_scangle_other 5.992 r_mcangle_it 4.881 r_mcangle_other 4.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.498 r_dihedral_angle_2_deg 18.48 r_dihedral_angle_6_deg 15.519 r_lrange_it 9.027 r_lrange_other 9.023 r_dihedral_angle_1_deg 8.041 r_scangle_it 5.994 r_scangle_other 5.992 r_mcangle_it 4.881 r_mcangle_other 4.88 r_scbond_it 4.044 r_scbond_other 4.043 r_mcbond_it 3.2 r_mcbond_other 3.191 r_angle_refined_deg 2.027 r_angle_other_deg 0.628 r_symmetry_xyhbond_nbd_refined 0.399 r_nbd_refined 0.226 r_xyhbond_nbd_refined 0.21 r_symmetry_nbd_refined 0.207 r_symmetry_nbd_other 0.204 r_nbtor_refined 0.184 r_nbd_other 0.171 r_symmetry_nbtor_other 0.092 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2310 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling Coot model building