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Crystal structure of SME-1 E166A in complex with cefsulodin
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 0.2M lithium chloride, 20% PEG4000
Crystal Properties Matthews coefficient Solvent content 2 38.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.268 α = 90 b = 51.046 β = 92.78 c = 131.316 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 2024-04-10 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 23.33 99.9 0.989 9.7 4.9 32693
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 2.05 0.624
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 22.403 32680 1636 99.869 0.204 0.2001 0.1977 0.268 0.2673 15.001
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] -0.615 -0.431 -2.462 3.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.498 r_dihedral_angle_2_deg 15.805 r_dihedral_angle_6_deg 14.207 r_lrange_it 11.789 r_dihedral_angle_1_deg 7.409 r_scangle_it 5.388 r_mcangle_it 4.54 r_scbond_it 3.516 r_rigid_bond_restr 3.411 r_mcbond_it 2.799
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.498 r_dihedral_angle_2_deg 15.805 r_dihedral_angle_6_deg 14.207 r_lrange_it 11.789 r_dihedral_angle_1_deg 7.409 r_scangle_it 5.388 r_mcangle_it 4.54 r_scbond_it 3.516 r_rigid_bond_restr 3.411 r_mcbond_it 2.799 r_angle_refined_deg 2.07 r_nbtor_refined 0.309 r_symmetry_nbd_refined 0.26 r_nbd_refined 0.223 r_symmetry_xyhbond_nbd_refined 0.204 r_xyhbond_nbd_refined 0.2 r_chiral_restr 0.139 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4108 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing