Experiment: 9SOJ

Protein with novel 3_1 knotted solenoid fold

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		277	0,1 M BICINE pH 9.0; 25% (w/v) PEG 3350 protein solution 7 mg/ml in 50 mM Tris, 200 mM NaCl, 5% glycerol, pH 8 (at 277 K)

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.09	α = 90
b = 82.302	β = 90
c = 88.05	γ = 90

Symmetry
Space Group	P 21 21 2

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		2025-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

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	1.88	48.51	99.7	0.997	12.81	12.79		49168			19.62

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	1.88	1.99			0.754	2.26

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	1.9	38.82	1.34	47668	2382	99.92	0.1653	0.1629	0.163	0.2114	0.2114	23.43

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	11.933
f_angle_d	0.8687
f_chiral_restr	0.0577
f_plane_restr	0.013
f_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3882
Nucleic Acid Atoms
Solvent Atoms	680
Heterogen Atoms	16

Software

Software
Software Name	Purpose
PHENIX	refinement
MxCuBE	data collection
XDS	data reduction
XDS	data scaling
PHASER	phasing
PHENIX	model building
Coot	model building