6HKV | pdb_00006hkv

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 malonate pH 5.0

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 138.4	α = 90
b = 145.705	β = 90
c = 149.453	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		2017-11-27	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	1.75	47.95	99.97	0.11	0.999	15.72	8.7		302337			26.26

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	1.75	1.81	99.9		1.78	0.48	1.29	9

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4u60	1.75	47.95	299628	3027	99.82	0.1761	0.1759	0.1842	0.201	0.2072	RANDOM	28.649

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]
0.28			-0.68		0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.369
r_dihedral_angle_4_deg	19.185
r_dihedral_angle_3_deg	11.864
r_dihedral_angle_1_deg	6.859
r_angle_refined_deg	1.302
r_angle_other_deg	0.938
r_chiral_restr	0.068
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.369
r_dihedral_angle_4_deg	19.185
r_dihedral_angle_3_deg	11.864
r_dihedral_angle_1_deg	6.859
r_angle_refined_deg	1.302
r_angle_other_deg	0.938
r_chiral_restr	0.068
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20567
Nucleic Acid Atoms
Solvent Atoms	2873
Heterogen Atoms	285

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
PDB_EXTRACT	data extraction
XDS	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.