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Crystal Structure of 2R, 3S-Xeruborbactam with SME-1
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 0.2M lithium chloride, 20%PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.05 40.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.98 α = 90 b = 51.237 β = 113.404 c = 74.856 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 2024-09-10 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 2.2 23.683 99.9 0.996 11.2 7.4 25335
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 0.753
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.2 23.683 25322 1261 99.89 0.19 0.187 0.2492 0.2181 20.912
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] -0.55 -0.425 -0.62 1.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.305 r_dihedral_angle_3_deg 17.211 r_dihedral_angle_6_deg 14.802 r_dihedral_angle_1_deg 7.332 r_lrange_it 6.464 r_scangle_it 4.622 r_scbond_it 3 r_mcangle_it 2.889 r_angle_refined_deg 2.155 r_mcbond_it 1.859
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.305 r_dihedral_angle_3_deg 17.211 r_dihedral_angle_6_deg 14.802 r_dihedral_angle_1_deg 7.332 r_lrange_it 6.464 r_scangle_it 4.622 r_scbond_it 3 r_mcangle_it 2.889 r_angle_refined_deg 2.155 r_mcbond_it 1.859 r_nbtor_refined 0.31 r_symmetry_nbd_refined 0.275 r_metal_ion_refined 0.248 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.205 r_symmetry_xyhbond_nbd_refined 0.194 r_chiral_restr 0.149 r_bond_refined_d 0.009 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4116 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing