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The structure of E. coli penicillin binding protein 3 (PBP3) in complex with a bicyclic peptide inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6I1I Piperacillin was removed
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 277 0.1M Tris pH 9.0 and 20% (w/v) PEG 6K supplemented with an additive, 30% (w/v) dextran sulphate sodium salt, Mr 5K
Crystal Properties Matthews coefficient Solvent content 2.11 42.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.89 α = 90 b = 152.181 β = 90 c = 43.675 γ = 90
Symmetry Space Group C 2 2 21
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 PILATUS 2M 2020-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.000 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.52 45.04 99.6 1 23.8 12.2 50525
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.52 1.55 93 0.749 7.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.52 45.04 50510 2525 99.58 0.184 0.1819 0.1915 0.2157 0.2257 24.42
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] 3.04 -1.971 -1.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.319 r_dihedral_angle_other_3_deg 17.939 r_dihedral_angle_4_deg 14.285 r_dihedral_angle_3_deg 13.146 r_dihedral_angle_1_deg 6.815 r_lrange_it 6.377 r_lrange_other 6.376 r_scangle_it 4.376 r_scangle_other 4.375 r_mcangle_it 3.241
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.319 r_dihedral_angle_other_3_deg 17.939 r_dihedral_angle_4_deg 14.285 r_dihedral_angle_3_deg 13.146 r_dihedral_angle_1_deg 6.815 r_lrange_it 6.377 r_lrange_other 6.376 r_scangle_it 4.376 r_scangle_other 4.375 r_mcangle_it 3.241 r_mcangle_other 3.241 r_scbond_it 2.848 r_scbond_other 2.847 r_mcbond_it 2.174 r_mcbond_other 2.169 r_angle_refined_deg 1.738 r_angle_other_deg 1.438 r_symmetry_nbd_refined 0.348 r_nbd_other 0.262 r_nbd_refined 0.228 r_xyhbond_nbd_refined 0.188 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.17 r_symmetry_xyhbond_nbd_refined 0.164 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.084 r_symmetry_xyhbond_nbd_other 0.075 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2525 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling Aimless data scaling PHASER phasing