Experiment: 9NY8

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	6.5	293.15	0.2 M sodium sulfate, 0.1 M bis-tris-propane (pH 6.5), and 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.53	α = 90
b = 125.53	β = 90
c = 122.31	γ = 120

Symmetry
Space Group	P 31 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	PIXEL	DECTRIS EIGER X 9M		2023-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 19-ID	0.978560	NSLS-II	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.1	43.84	94.1	0.045	0.999	15.7	30.5		47896

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	2.1	2.33			0.184	1.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.1	43.84	45573	2323	73.51	0.1937	0.19214	0.1961	0.22327	0.2261	RANDOM	59.92

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]
0.63	0.31		0.63		-2.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.006
r_long_range_B_refined	9.886
r_long_range_B_other	9.886
r_scangle_other	7.86
r_dihedral_angle_1_deg	6.128
r_mcangle_it	6.103
r_mcangle_other	6.103
r_scbond_it	5.414
r_scbond_other	5.276
r_mcbond_it	4.249

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.006
r_long_range_B_refined	9.886
r_long_range_B_other	9.886
r_scangle_other	7.86
r_dihedral_angle_1_deg	6.128
r_mcangle_it	6.103
r_mcangle_other	6.103
r_scbond_it	5.414
r_scbond_other	5.276
r_mcbond_it	4.249
r_mcbond_other	4.249
r_angle_refined_deg	1.058
r_angle_other_deg	0.37
r_chiral_restr	0.045
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5126
Nucleic Acid Atoms	1232
Solvent Atoms	58
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
STARANISO	data scaling
Aimless	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.