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Crystal structure of Penicillin-Binding Protein 1 (PBP1) from Staphylococcus aureus in complex with pentaglycine
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7O49
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 DL-malic acid
Crystal Properties Matthews coefficient Solvent content 3.96 68.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 313.993 α = 90 b = 198.186 β = 90 c = 220.903 γ = 90
Symmetry Space Group P 21 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 PILATUS 6M 2021-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 ALBA XALOC
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target
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 3.357 49.321 89.1 0.674 0.195 7.5 12.8 86448
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 3.357 3.756 2.723 0.785
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7O49 3.36 49.32 82133 4313 44.14 0.232 0.2301 0.2669 0.2303 RANDOM 97.202
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] 3.02 2.15 -5.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.621 r_dihedral_angle_3_deg 20.965 r_dihedral_angle_4_deg 14.743 r_dihedral_angle_1_deg 6.37 r_angle_refined_deg 1.558 r_angle_other_deg 1.439 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.621 r_dihedral_angle_3_deg 20.965 r_dihedral_angle_4_deg 14.743 r_dihedral_angle_1_deg 6.37 r_angle_refined_deg 1.558 r_angle_other_deg 1.439 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 47732 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 178
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction STARANISO data scaling PHASER phasing