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Crystal structure of Class A beta-lactamase BlaA in complex with ertapenem (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 2.29 45.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.743 α = 90 b = 72.818 β = 95.776 c = 43.7 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 2022-08-17 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 1.7 24.663 99.8 0.142 0.154 0.078 0.989 7.4 6.5 31443
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 1.7 1.73 0.591 0.682 0.332 0.809
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 1.7 24.663 31442 1608 99.791 0.196 0.1936 0.195 0.2298 0.2307 21.318
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] 2.066 0.45 -1.124 -1.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.008 r_dihedral_angle_3_deg 11.961 r_dihedral_angle_2_deg 10.633 r_lrange_it 8.981 r_dihedral_angle_1_deg 6.668 r_scangle_it 4.741 r_scbond_it 3.131 r_mcangle_it 2.396 r_angle_refined_deg 2.046 r_mcbond_it 1.711
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.008 r_dihedral_angle_3_deg 11.961 r_dihedral_angle_2_deg 10.633 r_lrange_it 8.981 r_dihedral_angle_1_deg 6.668 r_scangle_it 4.741 r_scbond_it 3.131 r_mcangle_it 2.396 r_angle_refined_deg 2.046 r_mcbond_it 1.711 r_nbtor_refined 0.31 r_nbd_refined 0.227 r_symmetry_nbd_refined 0.208 r_chiral_restr 0.171 r_xyhbond_nbd_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.138 r_bond_refined_d 0.01 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2004 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing