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Crystal Structure of SME-1 E166A in complex with cefoperazone
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 298 0.2 M Lithium Chloride, 20% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.15 42.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.594 α = 90 b = 51.352 β = 114.053 c = 77.997 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 2024-05-19 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 23.75 99.9 0.994 12.6 7.1 26555
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 0.744
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 23.183 26543 1274 99.842 0.166 0.1622 0.1622 0.2466 0.2467 20.956
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] -0.496 0.331 -0.899 0.786
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.984 r_dihedral_angle_3_deg 18.19 r_dihedral_angle_6_deg 15.431 r_lrange_it 11.631 r_scangle_it 7.786 r_dihedral_angle_1_deg 7.294 r_rigid_bond_restr 6.987 r_mcangle_it 5.76 r_scbond_it 5.413 r_mcbond_it 3.741
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.984 r_dihedral_angle_3_deg 18.19 r_dihedral_angle_6_deg 15.431 r_lrange_it 11.631 r_scangle_it 7.786 r_dihedral_angle_1_deg 7.294 r_rigid_bond_restr 6.987 r_mcangle_it 5.76 r_scbond_it 5.413 r_mcbond_it 3.741 r_angle_refined_deg 3.209 r_symmetry_nbd_refined 0.332 r_nbtor_refined 0.314 r_chiral_restr 0.308 r_nbd_refined 0.226 r_xyhbond_nbd_refined 0.194 r_ncsr_local_group_1 0.11 r_symmetry_xyhbond_nbd_refined 0.071 r_bond_refined_d 0.019 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4116 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing