8QL2

Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution: dark structure

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7YYQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.2M Ammonium sulfate, 0.1M Bis/Tris-methane pH=5.5, 21% PEG 3000 (m/v)

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.53	α = 90
b = 92.58	β = 96.71
c = 83.99	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	PIXEL	PSI JUNGFRAU 16M		2020-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SwissFEL ARAMIS BEAMLINE ESA	1.0	SwissFEL ARAMIS	ESA

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		injection

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	1.7	11.09	100	0.992	0.075	9.53	2089.8		123960			30.36

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	1.7	1.76	100		0.694	0.7885	1.43	1000.6

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	1.7	9.49	1.34	123589	1999	99.95	0.1619	0.1616	0.1808

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	16.113
f_angle_d	1.452
f_chiral_restr	0.103
f_bond_d	0.014
f_plane_restr	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7891
Nucleic Acid Atoms
Solvent Atoms	542
Heterogen Atoms	90

Software

Software
Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHENIX	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 R01GM157729.