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Crystal structure of Penicillin-Binding Protein 1 (PBP1) from Staphylococcus aureus in complex with piperacillin
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 D,L-malic acid
Crystal Properties Matthews coefficient Solvent content 4.66 73.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.688 α = 90 b = 178.688 β = 90 c = 223.652 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 PILATUS 6M 2019-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97925 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 3.028 47.397 95.1 0.328 0.058 14.3 32.1 26360
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 3.028 3.306 2.93 0.468
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 3.028 47.394 26360 1339 63.303 0.215 0.2116 0.2158 0.2778 0.2778 84.766
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] 0.651 0.326 0.651 -2.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.46 r_dihedral_angle_3_deg 22.176 r_dihedral_angle_4_deg 19.332 r_lrange_other 14.25 r_lrange_it 14.248 r_mcangle_it 11.038 r_mcangle_other 11.038 r_scangle_it 10.062 r_scangle_other 10.061 r_dihedral_angle_1_deg 7.248
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.46 r_dihedral_angle_3_deg 22.176 r_dihedral_angle_4_deg 19.332 r_lrange_other 14.25 r_lrange_it 14.248 r_mcangle_it 11.038 r_mcangle_other 11.038 r_scangle_it 10.062 r_scangle_other 10.061 r_dihedral_angle_1_deg 7.248 r_mcbond_it 7.006 r_mcbond_other 6.993 r_scbond_it 6.283 r_scbond_other 6.283 r_angle_refined_deg 1.543 r_angle_other_deg 1.174 r_nbd_other 0.301 r_symmetry_xyhbond_nbd_refined 0.29 r_nbd_refined 0.22 r_symmetry_nbd_refined 0.207 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.164 r_ncsr_local_group_1 0.13 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.059 r_symmetry_xyhbond_nbd_other 0.021 r_xyhbond_nbd_other 0.008 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7840 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling PHASER phasing