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Crystal structure of Penicillin-Binding Protein 1 (PBP1) from Staphylococcus aureus
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 3.92 68.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 311.862 α = 90 b = 197.148 β = 90 c = 221.596 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 2019-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 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 3.03 49.015 89.8 0.173 0.058 11 8.9 145321
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 3.033 3.416 1.195 0.401
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 5TRO 3.03 49 138083 7237 55.24 0.2128 0.2111 0.2457 0.2189 RANDOM 93.555
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] -0.01 1.27 -1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.676 r_dihedral_angle_3_deg 22.215 r_dihedral_angle_4_deg 19.638 r_dihedral_angle_1_deg 7.115 r_angle_refined_deg 1.517 r_angle_other_deg 1.213 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.676 r_dihedral_angle_3_deg 22.215 r_dihedral_angle_4_deg 19.638 r_dihedral_angle_1_deg 7.115 r_angle_refined_deg 1.517 r_angle_other_deg 1.213 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 48489 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 167
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction STARANISO data scaling PHASER phasing