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Crystal Structure of SME-1 E166A mutant in complex with Biapenem
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% PEG 4000
Crystal Properties Matthews coefficient Solvent content 1.73 29.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.605 α = 90 b = 51.728 β = 90 c = 88.226 γ = 90
Symmetry Space Group P 21 21 21
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 2023-10-11 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) R Merge I (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 1.4 22.37 99.3 0.063 0.999 18.6 6.6 40678
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 1.4 1.42 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.4 22.37 40618 1989 99.158 0.141 0.1388 0.1771 0.168 9.594
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] -2.456 1.101 1.355
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 21.982 r_dihedral_angle_6_deg 15.917 r_dihedral_angle_2_deg 12.625 r_dihedral_angle_3_deg 11.69 r_dihedral_angle_1_deg 7.011 r_rigid_bond_restr 5.745 r_scangle_it 5.701 r_scbond_it 4.019 r_mcangle_it 3.362 r_mcbond_it 2.241
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 21.982 r_dihedral_angle_6_deg 15.917 r_dihedral_angle_2_deg 12.625 r_dihedral_angle_3_deg 11.69 r_dihedral_angle_1_deg 7.011 r_rigid_bond_restr 5.745 r_scangle_it 5.701 r_scbond_it 4.019 r_mcangle_it 3.362 r_mcbond_it 2.241 r_angle_refined_deg 2.097 r_symmetry_xyhbond_nbd_refined 0.447 r_nbtor_refined 0.315 r_symmetry_nbd_refined 0.22 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.126 r_gen_planes_refined 0.012 r_bond_refined_d 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2044 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing