8OY7 | pdb_00008oy7

Time-resolved SFX structure of the class II photolyase complexed with a thymine dimer (10 nanosecond pump-probe delay)

X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5ZCW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		293	100 mM Amm sulfate, 100 mM Acetate pH 4.6, 4% PEG 4000, 10 mM Tris pH 7.5, 75 mM NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.2	α = 90
b = 117.76	β = 90
c = 170.47	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	PIXEL	PSI JUNGFRAU 16M		2022-07-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SwissFEL ARAMIS BEAMLINE ESA	1.035	SwissFEL ARAMIS	ESA

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	2.36	31.29	100	0.9829549	0.1154	8.086315	371.356332		58959			32.91

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)
	2.3602	2.401	100		0.579215	1.228	0.85	150.9	2890

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	2.36	31.29	1.39	48265	2447	82.3	0.3266	0.3221	0.32	0.4102	0.41	44.96

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	21.6164
f_angle_d	1.1951
f_chiral_restr	0.0579
f_bond_d	0.0106
f_plane_restr	0.0098

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7177
Nucleic Acid Atoms	1098
Solvent Atoms	212
Heterogen Atoms	111

Software

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