☰ Navigation Tabs
Crystal Structure of SME-1 E166A mutant in complex with Ertapenem
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, 0.2 M Lithium Chloride
Crystal Properties Matthews coefficient Solvent content 2.02 37.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.112 α = 90 b = 50.672 β = 92.521 c = 130.339 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 2024-07-23 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 2.32 23.952 99.9 0.994 11.8 5.6 20650
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 2.32 2.4 0.929
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 2.32 23.952 20634 1043 99.807 0.188 0.1833 0.1836 0.2802 0.2814 19.207
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] -0.797 -1.313 -0.51 1.417
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.932 r_dihedral_angle_6_deg 14.155 r_dihedral_angle_2_deg 13.054 r_lrange_it 9.642 r_dihedral_angle_1_deg 8 r_scangle_it 4.924 r_rigid_bond_restr 4.193 r_mcangle_it 3.896 r_scbond_it 3.162 r_angle_refined_deg 2.579
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.932 r_dihedral_angle_6_deg 14.155 r_dihedral_angle_2_deg 13.054 r_lrange_it 9.642 r_dihedral_angle_1_deg 8 r_scangle_it 4.924 r_rigid_bond_restr 4.193 r_mcangle_it 3.896 r_scbond_it 3.162 r_angle_refined_deg 2.579 r_mcbond_it 2.418 r_symmetry_nbd_refined 0.36 r_nbtor_refined 0.317 r_nbd_refined 0.246 r_xyhbond_nbd_refined 0.196 r_symmetry_xyhbond_nbd_refined 0.194 r_chiral_restr 0.172 r_ncsr_local_group_1 0.109 r_bond_refined_d 0.012 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4108 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing