Experiment: 9HFJ

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		293	0.1 M Potassium thiocyanate, 30% w/v Polyethylene glycol monomethyl ether 2,000

Crystal Properties
Matthews coefficient	Solvent content
2.2	43.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.084	α = 90
b = 62.084	β = 90
c = 53.202	γ = 120

Symmetry
Space Group	H 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 PILATUS 6M		2022-09-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.89844	Diamond	I04

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	1.4	23.99	99.7	0.046	0.051	0.022	1	21.4	9.8		15041

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)
	1.4	1.42	96.7		0.632	0.782	0.451	0.712	1.8	5.2

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.4	23.99	15038	773	99.735	0.176	0.1749	0.1758	0.2064	0.2067	22.406

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]
0.218	0.109		0.218		-0.707

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.478
r_dihedral_angle_3_deg	10.747
r_lrange_it	8.88
r_dihedral_angle_1_deg	6.845
r_scangle_it	4.928
r_scbond_it	3.602
r_mcangle_it	2.337
r_angle_refined_deg	2.195
r_mcbond_it	1.71
r_symmetry_nbd_refined	0.362

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.478
r_dihedral_angle_3_deg	10.747
r_lrange_it	8.88
r_dihedral_angle_1_deg	6.845
r_scangle_it	4.928
r_scbond_it	3.602
r_mcangle_it	2.337
r_angle_refined_deg	2.195
r_mcbond_it	1.71
r_symmetry_nbd_refined	0.362
r_nbtor_refined	0.298
r_xyhbond_nbd_refined	0.215
r_symmetry_xyhbond_nbd_refined	0.215
r_nbd_refined	0.21
r_chiral_restr	0.108
r_bond_refined_d	0.012
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	590
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms	38

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
DIALS	data collection
PHASER	phasing
Coot	model building

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.