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Ultra-high Resolution Crystal Structure of the CTX-M-15 Extended-Spectrum beta-Lactamase in Complex with Taniborbactam (VNRX-5133)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HBT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.1M Tris-HCl, 2.2-2.4M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.13 42.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.558 α = 90 b = 45.719 β = 90 c = 117.219 γ = 90
Symmetry Space Group P 21 21 21
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 2M 2015-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) 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 1.1 58.61 98.9 0.075 0.083 0.035 11.6 5.3 96837 96837
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 1.16 97.5 0.304 0.304 0.337 0.144 2.5 5.3
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 4HBT 1.1 58.61 92020 4746 98.76 0.1026 0.1016 0.1159 0.1208 0.1323 RANDOM 12.099
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 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 52.044 r_dihedral_angle_2_deg 37.272 r_sphericity_bonded 14.434 r_dihedral_angle_3_deg 11.969 r_dihedral_angle_4_deg 11.775 r_rigid_bond_restr 6.73 r_dihedral_angle_1_deg 5.9 r_angle_refined_deg 2.16 r_angle_other_deg 1.124 r_chiral_restr 0.15
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 52.044 r_dihedral_angle_2_deg 37.272 r_sphericity_bonded 14.434 r_dihedral_angle_3_deg 11.969 r_dihedral_angle_4_deg 11.775 r_rigid_bond_restr 6.73 r_dihedral_angle_1_deg 5.9 r_angle_refined_deg 2.16 r_angle_other_deg 1.124 r_chiral_restr 0.15 r_bond_refined_d 0.025 r_gen_planes_refined 0.013 r_bond_other_d 0.005 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1957 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing PDB_EXTRACT data extraction