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Crystal structure of SME-1 E166A in complex with cefprozil
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% PEG 4000
Crystal Properties Matthews coefficient Solvent content 1.99 38.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.067 α = 90 b = 51.245 β = 93.877 c = 131.15 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 2024-10-09 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) Rpim I (All) 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 2.3 22.09 99.9 0.049 0.996 12.7 8.8 21502
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 2.3 2.38 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 2.3 21.317 21486 1058 99.8 0.181 0.1766 0.1821 0.2665 0.2646 18.155
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] -0.825 0.87 1.902 -1.184
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.277 r_dihedral_angle_3_deg 16.731 r_dihedral_angle_2_deg 15.532 r_dihedral_angle_6_deg 14.087 r_dihedral_angle_1_deg 7.143 r_scangle_it 6.577 r_mcangle_it 5.413 r_scbond_it 4.244 r_rigid_bond_restr 3.482 r_mcbond_it 3.356
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.277 r_dihedral_angle_3_deg 16.731 r_dihedral_angle_2_deg 15.532 r_dihedral_angle_6_deg 14.087 r_dihedral_angle_1_deg 7.143 r_scangle_it 6.577 r_mcangle_it 5.413 r_scbond_it 4.244 r_rigid_bond_restr 3.482 r_mcbond_it 3.356 r_angle_refined_deg 1.896 r_nbtor_refined 0.304 r_symmetry_xyhbond_nbd_refined 0.257 r_nbd_refined 0.218 r_symmetry_nbd_refined 0.211 r_xyhbond_nbd_refined 0.182 r_chiral_restr 0.135 r_bond_refined_d 0.007 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4108 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing