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Crystal Structure of SME-1 E166A mutant in complex with Meropenem
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 2.06 38.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.311 α = 90 b = 51.08 β = 92.177 c = 130.829 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 2024-07-16 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 25.54 99.9 0.996 15.2 8.7 18976
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 0.941
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.4 25.54 18963 973 99.847 0.191 0.1874 0.2631 0.2443 16.634
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] -1.022 0.2 0.408 0.598
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.999 r_dihedral_angle_6_deg 14.289 r_dihedral_angle_2_deg 7.777 r_dihedral_angle_1_deg 7.573 r_lrange_it 6.127 r_rigid_bond_restr 2.241 r_angle_refined_deg 1.905 r_scangle_it 1.844 r_mcangle_it 1.497 r_scbond_it 1.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.999 r_dihedral_angle_6_deg 14.289 r_dihedral_angle_2_deg 7.777 r_dihedral_angle_1_deg 7.573 r_lrange_it 6.127 r_rigid_bond_restr 2.241 r_angle_refined_deg 1.905 r_scangle_it 1.844 r_mcangle_it 1.497 r_scbond_it 1.109 r_mcbond_it 0.885 r_nbtor_refined 0.307 r_nbd_refined 0.228 r_symmetry_nbd_refined 0.193 r_xyhbond_nbd_refined 0.191 r_symmetry_xyhbond_nbd_refined 0.143 r_chiral_restr 0.136 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4108 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing