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Crystal Structure of SME-1 carbapenemase in complex with Avibactam.
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% PEG 4000, Lithium Chloride 0.2M
Crystal Properties Matthews coefficient Solvent content 2.23 44.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.582 α = 90 b = 51.871 β = 114.112 c = 77.429 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 2024-06-11 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) 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 2.28 24.11 99.9 0.114 0.131 0.064 0.995 12.4 7.6 23927
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 2.28 24.11 0.037 0.043 0.021 0.999 6.7
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 2.28 23.18 23915 1154 99.858 0.159 0.1548 0.1544 0.2415 0.2443 16.815
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] 2.076 -0.595 0.505 -1.462
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.262 r_lrange_it 16.521 r_dihedral_angle_2_deg 15.527 r_dihedral_angle_6_deg 15.15 r_scangle_it 10.885 r_dihedral_angle_1_deg 8.871 r_scbond_it 7.671 r_rigid_bond_restr 7.361 r_mcangle_it 7.304 r_mcbond_it 4.684
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.262 r_lrange_it 16.521 r_dihedral_angle_2_deg 15.527 r_dihedral_angle_6_deg 15.15 r_scangle_it 10.885 r_dihedral_angle_1_deg 8.871 r_scbond_it 7.671 r_rigid_bond_restr 7.361 r_mcangle_it 7.304 r_mcbond_it 4.684 r_angle_refined_deg 2.737 r_nbtor_refined 0.317 r_symmetry_nbd_refined 0.295 r_nbd_refined 0.236 r_symmetry_xyhbond_nbd_refined 0.217 r_xyhbond_nbd_refined 0.189 r_chiral_restr 0.172 r_bond_refined_d 0.014 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4120 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement Coot model building CrysalisPro data reduction Aimless data scaling MOLREP phasing