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Crystal structure of C. difficile penicillin-binding protein 2 in complex with ceftobiprole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6G9F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 15% PEG 4000, 0.2 M AmSO4, 0.1 M Na Citrate pH 5.6
Crystal Properties Matthews coefficient Solvent content 4.18 70.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.7 α = 90 b = 196.39 β = 105.66 c = 70.97 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER X 16M 2021-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3 53.84 83.9 0.083 0.103 0.06 0.981 9.3 2.6 28449
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.16 81.6 0.539 0.677 0.405 0.675 2.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6g9f 3 50.01 26959 1483 83.47 0.2104 0.2073 0.2147 0.2664 0.2683 RANDOM 78.726
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] -2.12 3.08 -1.39 1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.115 r_dihedral_angle_4_deg 19.091 r_dihedral_angle_3_deg 18.918 r_dihedral_angle_1_deg 7.257 r_angle_refined_deg 1.466 r_angle_other_deg 1.239 r_chiral_restr 0.059 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.115 r_dihedral_angle_4_deg 19.091 r_dihedral_angle_3_deg 18.918 r_dihedral_angle_1_deg 7.257 r_angle_refined_deg 1.466 r_angle_other_deg 1.239 r_chiral_restr 0.059 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6479 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction MOSFLM data reduction MoRDa phasing