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Crystal structure of Penicillin-Binding Protein 1 (PBP1) from Staphylococcus aureus in complex with penicillin G
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TRO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 sodium citrate
Crystal Properties Matthews coefficient Solvent content 3.61 65.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.649 α = 90 b = 180.649 β = 90 c = 223.466 γ = 120
Symmetry Space Group P 64 2 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 PILATUS3 6M 2020-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97918 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.593 47.513 96.3 0.147 0.03 22.1 24.7 45182
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.593 2.846 2.163 0.42
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 5TRO 2.593 47.505 45181 2318 67.427 0.207 0.2048 0.2068 0.2415 0.2399 63.226
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] -0.084 -0.042 -0.084 0.273
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.978 r_dihedral_angle_3_deg 20.416 r_dihedral_angle_4_deg 19.05 r_lrange_other 11.96 r_lrange_it 11.957 r_scangle_it 9.043 r_scangle_other 9.019 r_mcangle_it 8.623 r_mcangle_other 8.623 r_dihedral_angle_1_deg 7.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.978 r_dihedral_angle_3_deg 20.416 r_dihedral_angle_4_deg 19.05 r_lrange_other 11.96 r_lrange_it 11.957 r_scangle_it 9.043 r_scangle_other 9.019 r_mcangle_it 8.623 r_mcangle_other 8.623 r_dihedral_angle_1_deg 7.014 r_scbond_it 5.866 r_scbond_other 5.825 r_mcbond_it 5.673 r_mcbond_other 5.664 r_angle_refined_deg 1.566 r_angle_other_deg 1.208 r_symmetry_xyhbond_nbd_refined 0.427 r_nbd_other 0.215 r_nbd_refined 0.207 r_symmetry_nbd_other 0.191 r_symmetry_nbd_refined 0.182 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.155 r_chiral_restr_other 0.142 r_ncsr_local_group_1 0.114 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.065 r_symmetry_xyhbond_nbd_other 0.023 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7755 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling MOLREP phasing