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Crystal structure of Antifungal agent Tavaborole 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, PEG 4000 20%
Crystal Properties Matthews coefficient Solvent content 2.23 44.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.235 α = 90 b = 51.153 β = 114.896 c = 78.318 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 2025-07-02 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 2.5 29.502 99.9 0.992 10.8 9.6 18229
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 2.5 2.6 0.9
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 2.5 29.502 18212 917 99.781 0.192 0.188 0.189 0.2684 0.2681 18.669
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] -0.508 -0.8 -1.092 1.637
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.066 r_dihedral_angle_6_deg 14.466 r_dihedral_angle_2_deg 12.032 r_dihedral_angle_1_deg 7.571 r_lrange_it 6.103 r_scangle_it 4.389 r_scbond_it 2.696 r_mcangle_it 2.528 r_angle_refined_deg 2.025 r_mcbond_it 1.541
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.066 r_dihedral_angle_6_deg 14.466 r_dihedral_angle_2_deg 12.032 r_dihedral_angle_1_deg 7.571 r_lrange_it 6.103 r_scangle_it 4.389 r_scbond_it 2.696 r_mcangle_it 2.528 r_angle_refined_deg 2.025 r_mcbond_it 1.541 r_nbtor_refined 0.31 r_symmetry_nbd_refined 0.27 r_nbd_refined 0.227 r_symmetry_xyhbond_nbd_refined 0.195 r_xyhbond_nbd_refined 0.193 r_chiral_restr 0.148 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4124 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing