Experiment: 8ESH

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5HHN	5HHN, 1S9W, 4QRT, 5VGE, 1Q94, 2BNR, 6RPB
experimental model	PDB	1S9W	5HHN, 1S9W, 4QRT, 5VGE, 1Q94, 2BNR, 6RPB
experimental model	PDB	4QRT	5HHN, 1S9W, 4QRT, 5VGE, 1Q94, 2BNR, 6RPB
experimental model	PDB	5VGE	5HHN, 1S9W, 4QRT, 5VGE, 1Q94, 2BNR, 6RPB
experimental model	PDB	1Q94	5HHN, 1S9W, 4QRT, 5VGE, 1Q94, 2BNR, 6RPB
experimental model	PDB	2BNR	5HHN, 1S9W, 4QRT, 5VGE, 1Q94, 2BNR, 6RPB
experimental model	PDB	6RPB	5HHN, 1S9W, 4QRT, 5VGE, 1Q94, 2BNR, 6RPB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	294.15	0.2 M Sodium Fluoride, 0.1 M BIS-TRIS propane pH 8.5, 20-24% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 147.373	α = 90
b = 147.373	β = 90
c = 147.373	γ = 90

Symmetry
Space Group	I 2 3

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 PILATUS3 6M		2022-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.979	APS	24-ID-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.72	104.21	99.9	0.102	0.105	0.024	0.999	24.9	17.4		14511			65.12

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.72	2.85	99.4		0.733	0.785	0.276	0.834		7.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	THROUGHOUT	5HHN, 1S9W, 4QRT, 5VGE, 1Q94, 2BNR, 6RPB	2.72	60.16	1.37	14510	1441	99.9	0.2194	0.2148	0.2595	63.0298

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3126
Nucleic Acid Atoms
Solvent Atoms	35
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
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.