Experiment: 8X0A

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, HANGING DROP	8.5	289	0.1 M Tris-HCl, and 2 M (NH4)2SO4

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.75	α = 90
b = 81.43	β = 107.356
c = 120.457	γ = 90

Symmetry
Space Group	I 1 2 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	CCD	ADSC QUANTUM 315r		2022-08-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.97902	SSRF	BL17U1

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	2.7	47.38	95.7	0.996	10.9	3.8		27862

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	2.7	2.83			0.688	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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	AlphaFold	2.7	47.38	27861	1380	99.376	0.231	0.2291	0.2783	48.104

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]
-0.289		0.47	1.699		-1.425

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.408
r_dihedral_angle_2_deg	17.562
r_dihedral_angle_6_deg	15.213
r_lrange_it	11.291
r_scangle_it	7.814
r_mcangle_it	7.504
r_dihedral_angle_1_deg	6.333
r_scbond_it	5.319
r_mcbond_it	5.006
r_angle_refined_deg	1.899

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.408
r_dihedral_angle_2_deg	17.562
r_dihedral_angle_6_deg	15.213
r_lrange_it	11.291
r_scangle_it	7.814
r_mcangle_it	7.504
r_dihedral_angle_1_deg	6.333
r_scbond_it	5.319
r_mcbond_it	5.006
r_angle_refined_deg	1.899
r_symmetry_xyhbond_nbd_refined	0.921
r_symmetry_nbd_refined	0.357
r_nbtor_refined	0.293
r_nbd_refined	0.221
r_xyhbond_nbd_refined	0.177
r_chiral_restr	0.11
r_gen_planes_refined	0.011
r_bond_refined_d	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7237
Nucleic Acid Atoms
Solvent Atoms	51
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASES	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.