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Crystal structure of SME-1 E166A in complex with cefotaxime
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, SITTING DROP 298 0.2 M lithium chloride, 20% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.13 42.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.481 α = 90 b = 51.5 β = 113.938 c = 77.024 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 2024-10-30 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 2.16 23.96 99.9 0.996 10.5 8.7 20261
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 2.16 2.23 0.887
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 21.981 20261 972 99.724 0.208 0.2053 0.2049 0.2715 0.281 24.909
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] -4.304 -2.241 -3.453 6.991
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 44.538 r_dihedral_angle_3_deg 17.294 r_dihedral_angle_6_deg 14.035 r_dihedral_angle_2_deg 12.477 r_scangle_it 8.834 r_mcangle_it 7.828 r_dihedral_angle_1_deg 7.367 r_rigid_bond_restr 6.735 r_scbond_it 5.923 r_mcbond_it 4.974
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 44.538 r_dihedral_angle_3_deg 17.294 r_dihedral_angle_6_deg 14.035 r_dihedral_angle_2_deg 12.477 r_scangle_it 8.834 r_mcangle_it 7.828 r_dihedral_angle_1_deg 7.367 r_rigid_bond_restr 6.735 r_scbond_it 5.923 r_mcbond_it 4.974 r_angle_refined_deg 1.846 r_symmetry_xyhbond_nbd_refined 0.359 r_nbtor_refined 0.309 r_symmetry_nbd_refined 0.237 r_xyhbond_nbd_refined 0.235 r_nbd_refined 0.232 r_chiral_restr 0.127 r_ncsr_local_group_1 0.053 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4108 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing