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Room temperature XFEL Isopenicillin N synthase structure in complex with the Fe(IV)=O mimic VO and ACV.
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BLZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 8.5 298 1.7 M Li2So4, 0.1 M TRIS pH8.5
Crystal Properties Matthews coefficient Solvent content 2.14 42.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.79 α = 90 b = 75.564 β = 90 c = 101.724 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 MX300-HS 2019-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL2 1.23997 SACLA BL2
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 injection
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 1.54 34.41 99.98 0.936 0.239 32.942 35.2 48446 20.66
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 1.54 1.566 99.92 0.026 1.269 0.706 11.56
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT FREE R-VALUE 1BLZ 1.54 34.41 1.3259 47861 1974 98.6784 0.1978 0.1966 0.198 0.2264 0.2284 29.4261
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 9.483413 f_angle_d 1.00168 f_chiral_restr 0.059667 f_bond_d 0.010258 f_plane_restr 0.007271
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2583 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 31
Software Software Software Name Purpose PHENIX refinement cctbx.xfel data reduction PHASER phasing cxi.merge data scaling