6HKU

Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1 in complex with sialylated precision glycooligomers

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4U60

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	PEG 3350, sodium maolante

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.277	α = 90
b = 146.16	β = 90
c = 150.413	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	PIXEL	DECTRIS PILATUS 2M-F		2018-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	1.98	49.05	99.8	0.29	0.995	8.52	10.5		212141			28.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.98	2.1	98.7		1.56	0.65	1.76	10.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4U60	1.98	49.05	210019	2122	99.76	0.1852	0.1847	0.2299	RANDOM	26.585

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]
-0.27			-1.55		1.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.899
r_dihedral_angle_4_deg	18.499
r_dihedral_angle_3_deg	11.847
r_dihedral_angle_1_deg	6.85
r_angle_refined_deg	1.301
r_angle_other_deg	0.881
r_chiral_restr	0.065
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.899
r_dihedral_angle_4_deg	18.499
r_dihedral_angle_3_deg	11.847
r_dihedral_angle_1_deg	6.85
r_angle_refined_deg	1.301
r_angle_other_deg	0.881
r_chiral_restr	0.065
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20664
Nucleic Acid Atoms
Solvent Atoms	2360
Heterogen Atoms	215

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data scaling

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 R01GM133198.