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Isopenicillin N synthase in complex with Fe and ACdV under anaerobic conditions
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZAE
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 2.13 42.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.681 α = 90 b = 75.325 β = 90 c = 101.717 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 2019-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER PAL-XFEL BEAMLINE NCI 1.318066 PAL-XFEL NCI
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 1.85 27.94 99.96 0.964 0.239 3.493 67.58 28105 23.14
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 1.85 1.88 100 0.1 1.166 0.578 16.25
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 1.85 27.94 1.33 27967 1994 99.55 0.2159 0.2135 0.2135 0.2457 0.2467 26.46
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 10.8967 f_angle_d 0.543 f_chiral_restr 0.0458 f_plane_restr 0.0041 f_bond_d 0.0027
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2596 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 35
Software Software Software Name Purpose PHENIX refinement cctbx.xfel data reduction cctbx.xfel.merge data scaling PHASER phasing