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Room temperature serial crystal structure of AmpC class C beta-lactamase, drop on fixed target from PAL-XFEL, 80 ms control (avibactam)
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6T3D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 293 Potassium phosphate (1.9 M, pH 8.8) with crystal seed
Crystal Properties Matthews coefficient Solvent content 2.59 52.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.967 α = 90 b = 77.599 β = 116.66 c = 99.25 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 CCD RAYONIX MX225-HS 2024-06-26 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 2.78 59.09 99.98 0.917 0.224 3.325 33.03 20500 41.48
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 2.78 2.8279 99.9 0.381 0.434 1.609 21.7
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 2.78 45.57 1.37 20407 1022 99.56 0.1598 0.1567 0.1588 0.2178 0.217 35.05
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 14.1857 f_angle_d 0.9965 f_chiral_restr 0.057 f_bond_d 0.0086 f_plane_restr 0.0063
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5598 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 5
Software Software Software Name Purpose PHENIX refinement DIALS data reduction DIALS data scaling PHENIX phasing