7YD8

TR-SFX MmCPDII-DNA complex: 2 ns snapshot. Includes 2 ns, dark, and extrapolated structure factors

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	4.6	296	100 mM Sodium Acetate pH 4.6 250 mM ammonium sulfate 4% PEG4000 (w/v) 50 mM DTT

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.47	α = 90
b = 115.93	β = 90
c = 169.35	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	PSI JUNGFRAU 16M		2021-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SwissFEL ARAMIS BEAMLINE ESA	1.0875	SwissFEL ARAMIS	ESA

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		injection

Injection
Diffraction ID	Description	Flow Rate	Injector Diameter	Injection Power	Injector Nozzle	Filter Size	Carrier Solvent
1	SwissFEL injector	4.2				20

Measurement
Diffraction ID	Pulse Duration	Pulse Repetition Rate	Focal Spot Size	Pulse Energy	Photons Per Pulse
1		100

Data Reduction
Diffraction ID	Frames Indexed	Crystal Hits	Total Frames
1	75274

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.07	16.78	100	0.996	10.21	1064.5		87484

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.07	2.09			0.501	1.92

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	7YC7	2.15	16.78	78141	3843	100	0.2342	0.2337	0.2432

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	20.785
f_angle_d	0.816
f_chiral_restr	0.117
f_bond_d	0.014
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7068
Nucleic Acid Atoms	1021
Solvent Atoms	379
Heterogen Atoms	111

Software

Software
Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
pointless	data scaling
REFMAC	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.