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Crystal structure of Class A beta-lactamase BlaA in complex with Meropenem (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 46.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.774 α = 90 b = 72.619 β = 94.953 c = 43.707 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 2022-10-05 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 2 24.53 99.9 0.199 0.199 0.091 0.991 8.2 10.9 19371
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 2.05 0.889
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 2 24.53 19370 940 99.871 0.21 0.2067 0.2084 0.2706 0.2727 22.059
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] 2.467 0.961 -1.27 -1.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.013 r_dihedral_angle_3_deg 12.694 r_dihedral_angle_2_deg 8.929 r_lrange_it 7.294 r_dihedral_angle_1_deg 6.642 r_scangle_it 3.871 r_scbond_it 2.53 r_mcangle_it 2.511 r_angle_refined_deg 1.805 r_mcbond_it 1.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.013 r_dihedral_angle_3_deg 12.694 r_dihedral_angle_2_deg 8.929 r_lrange_it 7.294 r_dihedral_angle_1_deg 6.642 r_scangle_it 3.871 r_scbond_it 2.53 r_mcangle_it 2.511 r_angle_refined_deg 1.805 r_mcbond_it 1.65 r_nbtor_refined 0.308 r_symmetry_xyhbond_nbd_refined 0.242 r_nbd_refined 0.23 r_xyhbond_nbd_refined 0.196 r_symmetry_nbd_refined 0.168 r_chiral_restr 0.139 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1992 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing