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Crystal structure of SME-1 E166A with cefovecin
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 0.2M lithium chloride, 20% PEG4000
Crystal Properties Matthews coefficient Solvent content 1.8 31.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.295 α = 90 b = 50.596 β = 98.033 c = 60.34 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 2024-11-11 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 2.1 21.54 99.2 0.997 11.2 4.9 12658
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 2.1 2.16 0.948
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 2.1 21.54 12642 587 98.789 0.18 0.1764 0.1778 0.2546 0.2556 24.88
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] -5.385 -4.945 2.443 4.171
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 24.489 r_dihedral_angle_2_deg 21.313 r_dihedral_angle_3_deg 18.015 r_dihedral_angle_6_deg 14.2 r_scangle_it 10.039 r_mcangle_it 7.732 r_dihedral_angle_1_deg 6.879 r_scbond_it 6.744 r_rigid_bond_restr 6.37 r_mcbond_it 4.929
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 24.489 r_dihedral_angle_2_deg 21.313 r_dihedral_angle_3_deg 18.015 r_dihedral_angle_6_deg 14.2 r_scangle_it 10.039 r_mcangle_it 7.732 r_dihedral_angle_1_deg 6.879 r_scbond_it 6.744 r_rigid_bond_restr 6.37 r_mcbond_it 4.929 r_angle_refined_deg 1.965 r_symmetry_nbd_refined 0.465 r_nbtor_refined 0.307 r_symmetry_xyhbond_nbd_refined 0.296 r_nbd_refined 0.222 r_xyhbond_nbd_refined 0.201 r_chiral_restr 0.138 r_gen_planes_refined 0.008 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2054 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing