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Isopenicillin N synthase in complex with Fe and Aad-Val-[(R)-1-amino-2-methylpropane-1-sulfonic acid]
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZAE Molecular replacement
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 2.07 40.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.23 α = 90 b = 74.49 β = 90 c = 101.01 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 2023-03-02 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) 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 1.8 41.8 100 0.339 0.353 0.995 0.095 6.7 13.4 29676 22.02
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 1.8 1.84 100 3.85 3.996 1.059 0.496 0.9
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.8 41.8 1.34 29597 1480 99.92 0.2083 0.2065 0.2418 0.2174 25.51
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 11.5592 f_angle_d 0.4818 f_chiral_restr 0.0427 f_plane_restr 0.0042 f_bond_d 0.0019
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2599 Nucleic Acid Atoms Solvent Atoms 274 Heterogen Atoms 36
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing