9SYA | pdb_00009sya

Crystal structure of HERV-K envelope glycoprotein surface subunit with cholates and sulfates bound

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-P61570-F1	Residues 111-430

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298.15	32.7% PEG 8K/ethylene glycol (1:2), 0.1 M MES/imidazole pH 6.5, 90 mM Morpheus NPS, and 1.572% (w/v) Morpheus III cholic acids

Crystal Properties
Matthews coefficient	Solvent content
3.15	60.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.04	α = 101.94
b = 63.52	β = 101.825
c = 70.681	γ = 104.061

Symmetry
Space Group	P 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 EIGER2 XE 16M	Focusing mirrors	2025-07-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9537	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.25	59.32	98.52	0.114	0.07	0.9785	11.41	3.7		44339			47.22

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.31	96.6		1.5	0.931	0.3167	0.7	3.5

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	2.25	59.32	1.96	44336	2016	98.32	0.2153	0.2129	0.2139	0.2672	0.267	61.48

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	17.9675
f_angle_d	1.2613
f_chiral_restr	0.0685
f_plane_restr	0.0092
f_bond_d	0.0083

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5127
Nucleic Acid Atoms
Solvent Atoms	292
Heterogen Atoms	486

Software

Software
Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing