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Crystal Structure of SME-1 Carbapenemase in Complex with Relebactam
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 20% PEG4000, 0.2M Lithium Chloride
Crystal Properties Matthews coefficient Solvent content 1.78 31.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.852 α = 90 b = 50.44 β = 99.866 c = 60.62 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 2024-06-05 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) R Merge I (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 2.2 25.22 99.9 0.124 0.995 10.6 7.5 10649
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 2.27 0.846
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.38 24.74 8422 421 99.799 0.17 0.1652 0.1669 0.2555 0.259 26.793
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] 0.449 1.046 -2.388 1.486
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.829 r_dihedral_angle_6_deg 14.238 r_dihedral_angle_2_deg 12.48 r_dihedral_angle_1_deg 8.714 r_lrange_it 6.287 r_scangle_it 4.179 r_scbond_it 2.846 r_mcangle_it 2.771 r_angle_refined_deg 2.709 r_mcbond_it 1.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.829 r_dihedral_angle_6_deg 14.238 r_dihedral_angle_2_deg 12.48 r_dihedral_angle_1_deg 8.714 r_lrange_it 6.287 r_scangle_it 4.179 r_scbond_it 2.846 r_mcangle_it 2.771 r_angle_refined_deg 2.709 r_mcbond_it 1.84 r_symmetry_nbd_refined 0.366 r_nbtor_refined 0.319 r_nbd_refined 0.248 r_xyhbond_nbd_refined 0.24 r_chiral_restr 0.171 r_symmetry_xyhbond_nbd_refined 0.164 r_bond_refined_d 0.012 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2062 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing