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Crystal structure of ADC-1-ertapenem complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9MTU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M lithium chloride, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.27 45.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.994 α = 90 b = 183.065 β = 98.48 c = 50.451 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 DECTRIS PILATUS 6M 2023-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.6 38.63 98.6 0.08 0.039 0.997 9.8 4 99666
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 0.577 0.491 1.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 1.6 38.63 1.37 99491 4946 98.43 0.1837 0.1825 0.1825 0.2069 0.2069
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.761 f_angle_d 0.982 f_chiral_restr 0.062 f_plane_restr 0.007 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5573 Nucleic Acid Atoms Solvent Atoms 395 Heterogen Atoms 74
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling MOLREP phasing