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Crystal Structure of SME-1 E166A Mutant in complex with Cefaclor
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, 0.2M Lithium Chloride
Crystal Properties Matthews coefficient Solvent content 1.86 34.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.297 α = 90 b = 50.788 β = 98.634 c = 61.91 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 2024-06-03 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 2.4 23.46 97 0.993 10.9 3.9 8331
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 2.4 2.49 0.925
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 2.4 21.476 8321 389 96.666 0.156 0.1509 0.151 0.2624 0.2649 22.131
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] -0.526 0.49 -1.32 1.623
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.673 r_dihedral_angle_6_deg 14.599 r_dihedral_angle_2_deg 14.592 r_lrange_it 10.824 r_dihedral_angle_1_deg 8.306 r_scangle_it 5.782 r_rigid_bond_restr 5.205 r_mcangle_it 5.114 r_scbond_it 3.803 r_mcbond_it 3.167
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.673 r_dihedral_angle_6_deg 14.599 r_dihedral_angle_2_deg 14.592 r_lrange_it 10.824 r_dihedral_angle_1_deg 8.306 r_scangle_it 5.782 r_rigid_bond_restr 5.205 r_mcangle_it 5.114 r_scbond_it 3.803 r_mcbond_it 3.167 r_angle_refined_deg 2.761 r_symmetry_nbd_refined 0.354 r_nbtor_refined 0.31 r_nbd_refined 0.242 r_symmetry_xyhbond_nbd_refined 0.209 r_chiral_restr 0.189 r_xyhbond_nbd_refined 0.16 r_bond_refined_d 0.014 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2058 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing