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Isopenicillin N synthase Q280A and L282A variant in complex with Fe and ACV under anaerobic conditions.
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 8.3 293 1.7 M Li2SO4, 0.1 M Tris pH 8.3
Crystal Properties Matthews coefficient Solvent content 1.98 37.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.234 α = 90 b = 73.699 β = 90 c = 100.25 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 100 PIXEL DECTRIS EIGER2 XE 16M 2024-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.68 59.38 100 0.163 0.176 0.066 0.998 9.6 13.2 34828 21.76
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.68 1.71 100 3.022 3.257 1.207 0.526 0.8 13.8
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 1.68 59.38 1.33 34828 3772 99.77 0.1986 0.1971 0.1971 0.2228 0.2229 27.16
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 11.9886 f_angle_d 0.567 f_chiral_restr 0.0456 f_plane_restr 0.0051 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2539 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement xia2 data reduction Aimless data scaling PHASER phasing