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Isopenicillin N synthase structure in complex with Fe and IPN exposed to dioxygen.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BLZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 8.5 298 1.7 M Li2SO4, 0.1 M TRIS pH8.5
Crystal Properties Matthews coefficient Solvent content 2.06 42.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.01 α = 90 b = 74.53 β = 90 c = 101.11 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 PILATUS 6M-F 2018-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
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 1.66 33.7 100 0.208 0.217 0.06 0.998 9.2 12.9 37503 19.4
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 1.66 1.7 100 2.858 2.969 0.798 0.593 1 13.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 THROUGHOUT 1BLZ 1.66 31.849 1.33 37426 1880 99.94 0.1792 0.1771 0.1774 0.2175 0.2177 28.3343
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 11.183 f_angle_d 0.757 f_chiral_restr 0.052 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2580 Nucleic Acid Atoms Solvent Atoms 308 Heterogen Atoms 59
Software Software Software Name Purpose PHENIX refinement xia2 data reduction Aimless data scaling PHASER phasing