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Crystal Structure of SME-1 E166A with cefpirome
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 1.81 31.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.516 α = 90 b = 49.888 β = 99.298 c = 61.153 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 2024-03-05 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 25.82 99.9 0.997 13.2 7.8 14812
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 0.921
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 25.82 14794 739 99.838 0.159 0.1558 0.1541 0.2195 0.2225 17.842
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] -0.763 -2.586 -0.352 1.862
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 24.447 r_lrange_other 24.325 r_dihedral_angle_2_deg 17.19 r_dihedral_angle_3_deg 16.676 r_dihedral_angle_6_deg 15.191 r_scangle_it 7.461 r_scangle_other 7.441 r_dihedral_angle_1_deg 6.69 r_dihedral_angle_other_2_deg 5.42 r_mcangle_other 5.121
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 24.447 r_lrange_other 24.325 r_dihedral_angle_2_deg 17.19 r_dihedral_angle_3_deg 16.676 r_dihedral_angle_6_deg 15.191 r_scangle_it 7.461 r_scangle_other 7.441 r_dihedral_angle_1_deg 6.69 r_dihedral_angle_other_2_deg 5.42 r_mcangle_other 5.121 r_mcangle_it 5.115 r_scbond_it 4.862 r_scbond_other 4.844 r_rigid_bond_restr 3.644 r_mcbond_it 3.235 r_mcbond_other 3.181 r_angle_refined_deg 1.917 r_angle_other_deg 0.625 r_symmetry_xyhbond_nbd_other 0.269 r_nbd_other 0.268 r_xyhbond_nbd_refined 0.241 r_symmetry_nbd_refined 0.226 r_nbd_refined 0.219 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.181 r_symmetry_xyhbond_nbd_refined 0.141 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2054 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing