Experiment: 9NY7

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	4	293.15	0.2 M sodium malonate (pH 4.0) and 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 177.461	α = 90
b = 87.353	β = 100.378
c = 130.942	γ = 90

Symmetry
Space Group	C 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	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	0.979493	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	2.07	33.82	92.1	0.118	0.985	4.8	3.5		72942

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	2.07	2.367			0.573

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	2.07	33.82	70230	3661	61.43	0.19361	0.19147	0.2005	0.23438	0.2399	RANDOM	45.886

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]
-0.3		-0.13	0.34		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.553
r_long_range_B_other	12.832
r_long_range_B_refined	12.817
r_scangle_other	10.905
r_mcangle_it	8.03
r_mcangle_other	8.03
r_scbond_it	7.904
r_scbond_other	7.904
r_dihedral_angle_1_deg	7.078
r_mcbond_it	5.565

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.553
r_long_range_B_other	12.832
r_long_range_B_refined	12.817
r_scangle_other	10.905
r_mcangle_it	8.03
r_mcangle_other	8.03
r_scbond_it	7.904
r_scbond_other	7.904
r_dihedral_angle_1_deg	7.078
r_mcbond_it	5.565
r_mcbond_other	5.565
r_angle_refined_deg	1.247
r_angle_other_deg	0.438
r_chiral_restr	0.061
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13378
Nucleic Acid Atoms
Solvent Atoms	421
Heterogen Atoms	60

Software

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