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Crystal structure of SME-1 E166A with cefotetan
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% PEG4000, 0.2M lithium chloride
Crystal Properties Matthews coefficient Solvent content 1.79 31.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.988 α = 90 b = 50.511 β = 97.836 c = 60.163 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 2024-03-05 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 2.2 23.25 99.9 0.994 11 8.2 10993
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 2.27 0.904
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 2.2 23.25 10979 560 99.836 0.169 0.165 0.168 0.2505 0.2493 27.524
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] 2.382 -3.764 1.996 -3.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.707 r_lrange_it 18.175 r_dihedral_angle_3_deg 16.821 r_dihedral_angle_6_deg 14.782 r_scangle_it 11.028 r_mcangle_it 9.338 r_scbond_it 7.331 r_dihedral_angle_1_deg 7.042 r_mcbond_it 5.908 r_rigid_bond_restr 3.943
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.707 r_lrange_it 18.175 r_dihedral_angle_3_deg 16.821 r_dihedral_angle_6_deg 14.782 r_scangle_it 11.028 r_mcangle_it 9.338 r_scbond_it 7.331 r_dihedral_angle_1_deg 7.042 r_mcbond_it 5.908 r_rigid_bond_restr 3.943 r_angle_refined_deg 1.897 r_nbtor_refined 0.305 r_symmetry_nbd_refined 0.242 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.225 r_symmetry_xyhbond_nbd_refined 0.182 r_chiral_restr 0.117 r_bond_refined_d 0.006 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2054 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing