☰ Navigation Tabs
Crystal Structure of SME-1 E166A mutant in complex with Doripenem
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, 0.2M Lithium Chloride
Crystal Properties Matthews coefficient Solvent content 2.16 41.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.743 α = 90 b = 51.768 β = 114.216 c = 75.004 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 2.5 28.553 99.2 0.996 16.6 7.9 17497
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 2.5 2.6 0.994
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 2.5 28.553 17482 907 99.071 0.213 0.209 0.2093 0.2913 0.2935 9.364
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] 0.826 -0.643 -0.202 -0.033
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 24.577 r_dihedral_angle_3_deg 17.647 r_dihedral_angle_6_deg 15.193 r_mcangle_it 11.009 r_dihedral_angle_2_deg 9.496 r_mcbond_it 7.541 r_dihedral_angle_1_deg 7.496 r_scangle_it 6.011 r_rigid_bond_restr 4.461 r_scbond_it 3.839
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 24.577 r_dihedral_angle_3_deg 17.647 r_dihedral_angle_6_deg 15.193 r_mcangle_it 11.009 r_dihedral_angle_2_deg 9.496 r_mcbond_it 7.541 r_dihedral_angle_1_deg 7.496 r_scangle_it 6.011 r_rigid_bond_restr 4.461 r_scbond_it 3.839 r_angle_refined_deg 2.549 r_symmetry_xyhbond_nbd_refined 0.387 r_nbtor_refined 0.315 r_symmetry_nbd_refined 0.274 r_nbd_refined 0.238 r_xyhbond_nbd_refined 0.206 r_chiral_restr 0.17 r_ncsr_local_group_1 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4108 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing