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Crystal Structure of Vaborbactam in complex with SME-1 class A Carbapenemase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DY6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M lithium chloride, 20% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.04 39.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.039 α = 90 b = 51.011 β = 92.799 c = 130.533 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 RIGAKU HyPix-6000HE 2024-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2 23.92 99.9 0.996 14.7 6.7 32253
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 0.898
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 23.764 32240 1604 99.827 0.188 0.1849 0.2418 0.2243 14.347
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] 2.094 0.271 1.881 -3.983
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 27.084 r_dihedral_angle_3_deg 16.957 r_dihedral_angle_6_deg 13.859 r_dihedral_angle_2_deg 9.532 r_dihedral_angle_1_deg 6.879 r_rigid_bond_restr 5.36 r_scangle_it 4.519 r_mcangle_it 3.721 r_scbond_it 2.97 r_mcbond_it 2.268
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 27.084 r_dihedral_angle_3_deg 16.957 r_dihedral_angle_6_deg 13.859 r_dihedral_angle_2_deg 9.532 r_dihedral_angle_1_deg 6.879 r_rigid_bond_restr 5.36 r_scangle_it 4.519 r_mcangle_it 3.721 r_scbond_it 2.97 r_mcbond_it 2.268 r_angle_refined_deg 1.928 r_nbtor_refined 0.309 r_symmetry_nbd_refined 0.294 r_nbd_refined 0.226 r_symmetry_xyhbond_nbd_refined 0.219 r_xyhbond_nbd_refined 0.192 r_chiral_restr 0.126 r_gen_planes_refined 0.008 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4123 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing