7B6T

Sheep Polyomavirus VP1 in complex with 10 mM globo-N-tetraose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6Y61

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
3.56	65.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.274	α = 90
b = 130.274	β = 90
c = 222.145	γ = 120

Symmetry
Space Group	P 31

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	PIXEL	DECTRIS PILATUS 2M-F		2019-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.00004	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	1.7	48.91	99.9	0.107	0.998	13.51	5.78		462792			27.9

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	1.7	1.8			1.085	0.485	1.61

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6Y61	1.701	48.908	458240	4550	99.951	0.144	0.1433	0.1651	22.373

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]
-2.032			-2.032		4.065

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.195
r_dihedral_angle_4_deg	24.061
r_dihedral_angle_3_deg	11.507
r_dihedral_angle_1_deg	7.446
r_lrange_it	5.153
r_lrange_other	4.854
r_scangle_it	2.983
r_scangle_other	2.983
r_angle_other_deg	2.543
r_mcangle_it	2.493
r_mcangle_other	2.493
r_scbond_it	2.087
r_scbond_other	2.086
r_mcbond_it	1.727
r_mcbond_other	1.727
r_angle_refined_deg	1.635
r_metal_ion_refined	0.275
r_nbd_other	0.272
r_symmetry_nbd_other	0.216
r_nbd_refined	0.2
r_symmetry_nbd_refined	0.185
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.155
r_symmetry_xyhbond_nbd_refined	0.143
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.079
r_symmetry_xyhbond_nbd_other	0.072
r_bond_other_d	0.036
r_gen_planes_other	0.015
r_bond_refined_d	0.009
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20328
Nucleic Acid Atoms
Solvent Atoms	3203
Heterogen Atoms	411

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building