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Isopenicillin N synthase in complex with Fe and IPN using tr-SSX
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 2.14 42.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.915 α = 90 b = 75.236 β = 90 c = 101.841 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 PIXEL DECTRIS PILATUS3 6M 2025-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.999850 Diamond I24
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 undefined (fs) undefined (KeV)
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 1.9 60.51 99.96 0.931322 0.261 2.003 31.61 26112 29.96
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 1.9 1.9328 100 0.24242 0.957 0.572 22.78
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 MOLECULAR REPLACEMENT FREE R-VALUE 1.9 60.51 1.33 25671 2000 98.31 0.2064 0.2036 0.2037 0.2379 0.2381 36.05
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 12.1743 f_angle_d 0.492 f_chiral_restr 0.0437 f_plane_restr 0.004 f_bond_d 0.0022
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2584 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 30
Software Software Software Name Purpose PHENIX refinement PHENIX refinement DIALS data reduction DIALS data scaling PHASER phasing