Experiment: 8FII

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5KEG	Stripped of water, Zn2+, Cl- and ssDNA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.6	285	A3A (50 mM MES pH 6.0, 100 mM NaCl, 1 mM TCEP, 0.2 mM EDTA) was mixed with oligonucleotides (10 mM Tris/HCl pH 7.9, 1 mM EDTA) at 0.85 mM and 1.7 mM respectively. Dilution was done with protein buffer. The mixture was added to crystallization liquid 1 to 1 and the mixture was pipetted on siliconized glass disks and sealed on top of a reservoir of crystallization liquid for hanging drop crystallization at 12 degrees Celsius. The crystallization liquid has the following composition: 100 mM Bicine at pH 6.6, 200 mM NaCl, 20 mM putrescine, 1 mM TCEP, 1 mM inositol hexa phosphate (phytic acid) and 45 % pentaerythritol propoxylate (5/4 PO/OH)

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.323	α = 90
b = 57.197	β = 99.37
c = 91.422	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	100	PIXEL	DECTRIS EIGER X 16M	1 vertical and 2 horizontal focussing mirrors	2021-09-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.953739	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.94	49.05	99	0.166	0.094	0.985	5.8	3.9		11619			42.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.94	3.12	97.1		0.583	0.338	0.918	2.2	3.9

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5KEGf	2.94	48.35	11041	567	98.93	0.2542	0.2512	0.26	0.3103	0.32	RANDOM	54.095

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]
7.43		6.32	-5.56		-3.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.431
r_dihedral_angle_4_deg	20.662
r_dihedral_angle_3_deg	17.638
r_dihedral_angle_1_deg	6.361
r_angle_refined_deg	1.78
r_angle_other_deg	1.4
r_chiral_restr	0.099
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2892
Nucleic Acid Atoms	448
Solvent Atoms
Heterogen Atoms	37

Software

Software
Software Name	Purpose
XDS	data reduction
JBluIce-EPICS	data collection
Aimless	data scaling
pointless	data scaling
MOLREP	phasing
REFMAC	refinement
Coot	model building

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.