8PY7

Isopenicillin N synthase in complex with Fe, ACdV and O2 after 1s O2 exposure

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6ZAM	molecular replacement

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	42.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.758	α = 90
b = 75.376	β = 90
c = 101.764	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	293	CCD	RAYONIX MX340-HS		2021-03-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE MFX	1.300289	SLAC LCLS	MFX

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	1.49	22.53	99.95	0.997	0.067	6.379	186.07		53297			19.04

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	1.49	1.52	99.85		0.329	0.861	0.581	12.31

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.49	22.53	1.33	53244	1999	99.89	0.1511	0.15	0.1805	27.49

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	12.1283
f_angle_d	0.9886
f_chiral_restr	0.0803
f_plane_restr	0.0078
f_bond_d	0.0073

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2597
Nucleic Acid Atoms
Solvent Atoms	207
Heterogen Atoms	37

Software

Software
Software Name	Purpose
PHENIX	refinement
cctbx.xfel	data reduction
cctbx.xfel.merge	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.