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Isopenicillin N synthase in complex with Fe and ACV
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8PY6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 8.5 293 1.7 M Li2SO4, 0.1 M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.11 42.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.834 α = 90 b = 75.521 β = 90 c = 101.806 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 MX340-HS 2025-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE MFX 1.282235 SLAC LCLS MFX
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 ADE Tape drive injection
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 35 (fs) 30 undefined (KeV)
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 ADE Tape drive undefined (µl/min) undefined (µm)
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 1.45 22.57 99.96 0.988419 0.12 5.5 52.48 57981
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 1.45 1.475 99.93 0.389263 0.795 1.064 12.31
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.45 22.57 57981 2000 99.99 0.1533 0.1525 0.1525 0.1757 0.1756 24.46
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 12.5886 f_angle_d 1.2313 f_chiral_restr 0.1058 f_bond_d 0.0138 f_plane_restr 0.0101
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2622 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 35
Software Software Software Name Purpose PHENIX refinement cctbx.xfel data reduction cctbx.xfel.merge data scaling PHASER phasing