☰ Navigation Tabs
Crystal Structure of Ledaborbactam in complex with SME-1 class A Carbapenemase
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 0.2 M lithium chloride, PEG 4000 20%
Crystal Properties Matthews coefficient Solvent content 2.02 39.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.391 α = 90 b = 50.465 β = 97.722 c = 130.588 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 2024-12-30 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 21.78 99.9 0.994 8.9 7.5 24125
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 0.846
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 21.577 24098 1209 99.797 0.196 0.193 0.2009 0.2547 0.2575 16.836
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] 1.706 -0.156 -2.672 0.973
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 31.743 r_dihedral_angle_3_deg 17.791 r_dihedral_angle_2_deg 15.582 r_dihedral_angle_6_deg 13.401 r_scangle_it 7.287 r_dihedral_angle_1_deg 6.722 r_mcangle_it 5.557 r_scbond_it 4.761 r_rigid_bond_restr 4.571 r_mcbond_it 3.468
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 31.743 r_dihedral_angle_3_deg 17.791 r_dihedral_angle_2_deg 15.582 r_dihedral_angle_6_deg 13.401 r_scangle_it 7.287 r_dihedral_angle_1_deg 6.722 r_mcangle_it 5.557 r_scbond_it 4.761 r_rigid_bond_restr 4.571 r_mcbond_it 3.468 r_angle_refined_deg 1.786 r_nbtor_refined 0.306 r_symmetry_nbd_refined 0.244 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.193 r_chiral_restr 0.117 r_symmetry_xyhbond_nbd_refined 0.095 r_ncsr_local_group_1 0.045 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4116 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing