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Room temperature serial crystal structure of CTX-M-15 class A beta-lactamase, drop on fixed target from PAL-XFEL, 1.3 s checkerboard control (avibactam)
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BH6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 2.0 M ammonium sulphate, 0.1 M Tris 8.0, with crystal seed
Crystal Properties Matthews coefficient Solvent content 2.18 43.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.27 α = 90 b = 45.877 β = 90 c = 118.646 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 CCD RAYONIX MX225-HS 2024-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER PAL-XFEL BEAMLINE NCI 1.3042 PAL-XFEL NCI
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 silicon 'Oxford' chip fixed target
Fixed Target Diffraction ID Description Sample Holding Support Base Motion control Details Sample Solvent 1 drop on fixed target
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) R Split (All) 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 1.47 59.32 100 0.956 0.195 3.043 63.01 44875 18
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.47 1.4953 100 0.381 0.892 0.654 17.33
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 1.47 42.79 1.33 42833 2011 99.79 0.1587 0.157 0.1567 0.1933 0.1931 23.62
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 12.5211 f_angle_d 0.7243 f_chiral_restr 0.0723 f_plane_restr 0.007 f_bond_d 0.0045
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1943 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 12
Software Software Software Name Purpose PHENIX refinement DIALS data reduction DIALS data scaling PHENIX phasing