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Crystal structure of Class A beta-lactamase BlaA in complex with Tebipenem (imine form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5E2E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1 M TRIS hydrochloride pH 8.5, 2.0 M Ammonium phosphate monobasic
Crystal Properties Matthews coefficient Solvent content 2.25 44.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.342 α = 90 b = 72.182 β = 96.087 c = 43.543 γ = 90
Symmetry Space Group C 1 2 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 2022-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54184
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 1.5 27.92 99.9 0.104 0.111 0.038 0.998 14 13.7 44966
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 0.368 0.657
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5E2E 1.5 24.597 44951 2244 99.896 0.174 0.1729 0.1737 0.2039 0.2045 17.047
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] 1.187 0.057 -0.599 -0.587
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.567 r_dihedral_angle_6_deg 14.644 r_dihedral_angle_3_deg 12.048 r_lrange_it 7.275 r_dihedral_angle_1_deg 6.187 r_scangle_it 4.864 r_scbond_it 3.243 r_mcangle_it 2.225 r_angle_refined_deg 2.218 r_mcbond_it 1.513
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.567 r_dihedral_angle_6_deg 14.644 r_dihedral_angle_3_deg 12.048 r_lrange_it 7.275 r_dihedral_angle_1_deg 6.187 r_scangle_it 4.864 r_scbond_it 3.243 r_mcangle_it 2.225 r_angle_refined_deg 2.218 r_mcbond_it 1.513 r_nbtor_refined 0.318 r_symmetry_nbd_refined 0.26 r_symmetry_xyhbond_nbd_refined 0.23 r_nbd_refined 0.226 r_xyhbond_nbd_refined 0.202 r_chiral_restr 0.141 r_bond_refined_d 0.011 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2012 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing