7B6V

Sheep Polyomavirus VP1 in complex with 5 mM Forssman antigen pentaose and 20 mM 3'-sialyllactosamine

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
3.55	65.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.404	α = 90
b = 130.404	β = 90
c = 221.221	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		2019-10-19	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	1.798	48.85	99.8	0.162	0.997	11.02	9.9		390469			28.5

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	1.8	1.91			1.273	0.471	1.51

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	1.798	48.846	390439	6588	99.8	0.153	0.1521	0.177	24.646

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]
0.211			0.211		-0.421

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.663
r_dihedral_angle_4_deg	21.198
r_dihedral_angle_3_deg	12.888
r_dihedral_angle_1_deg	7.932
r_lrange_it	4.512
r_lrange_other	4.362
r_scangle_it	2.969
r_scangle_other	2.969
r_angle_other_deg	2.861
r_mcangle_it	2.764
r_mcangle_other	2.763
r_scbond_it	2.153
r_scbond_other	2.153
r_mcbond_it	2.036
r_mcbond_other	2.036
r_angle_refined_deg	1.721
r_nbd_other	0.276
r_symmetry_nbd_other	0.216
r_nbd_refined	0.183
r_symmetry_xyhbond_nbd_refined	0.171
r_nbtor_refined	0.166
r_xyhbond_nbd_refined	0.165
r_metal_ion_refined	0.152
r_symmetry_nbd_refined	0.121
r_symmetry_nbtor_other	0.097
r_chiral_restr	0.079
r_symmetry_xyhbond_nbd_other	0.068
r_bond_other_d	0.035
r_gen_planes_other	0.014
r_bond_refined_d	0.009
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20301
Nucleic Acid Atoms
Solvent Atoms	2352
Heterogen Atoms	665

Software

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