Experiment: 8PHA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	15%(w/v) PEG 3K, 20%(v/v) 1,2,4-butanetriol, 1%(w/v) NDSB 256 0.01 M of each Polyamine 0.1 M GlyGly/AMPD. AMPD: 2-amino-2-methyl-1,3-propanediol; NDSB 256 Surfactant (PDB ID: DMX) Polyamine: Spermine 4 HCl (PDB ID: SPM), Sermidine 3 HCl (PDB ID: SPD), 1,4Diaminobutane 2 HCl (PDB ID:PUT), DL-Ornithine HCl (PDB ID:ORD/ORN)

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.363	α = 90
b = 109.116	β = 90
c = 192.925	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	100	PIXEL	DECTRIS EIGER X 16M		2022-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.00001	SLS	X06SA

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	2.02	48.23	96.5	0.092	0.101	0.042	0.999	9.5	5.8		119562			30.45

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	2.02	2.09			0.891	0.978	0.395	0.715	2.1	5.9

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	2.02	48.23	1.34	119325	5948	88.47	0.1728	0.1707	0.1811	0.2123	0.218	38.62

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	14.2368
f_angle_d	0.7699
f_chiral_restr	0.0482
f_plane_restr	0.0069
f_bond_d	0.0057

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14167
Nucleic Acid Atoms
Solvent Atoms	1215
Heterogen Atoms	72

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	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.