7B6S

Sheep Polyomavirus VP1 in complex with 10 mM Forssman antigen pentaose

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
3.58	65.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.494	α = 90
b = 130.494	β = 90
c = 222.435	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		2019-08-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.0077	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	1.85	42.72	99.8	0.105	0.998	14.42	6.75		361163			32.4

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	1.85	1.96	98.8		1.045	0.99	1.77	6.01

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	1.923	42.714	317860	3205	99.782	0.15	0.1493	0.1757	28.073

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]
-7.491			-7.491		14.981

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.19
r_dihedral_angle_4_deg	20.32
r_dihedral_angle_3_deg	12.475
r_dihedral_angle_1_deg	7.724
r_lrange_it	5.116
r_lrange_other	4.948
r_scangle_it	3.607
r_scangle_other	3.607
r_mcangle_it	3.078
r_mcangle_other	3.078
r_scbond_it	2.625
r_scbond_other	2.625
r_angle_other_deg	2.582
r_mcbond_it	2.301
r_mcbond_other	2.3
r_angle_refined_deg	1.643
r_nbd_other	0.272
r_symmetry_nbd_other	0.213
r_symmetry_nbd_refined	0.2
r_nbd_refined	0.187
r_nbtor_refined	0.166
r_xyhbond_nbd_refined	0.16
r_symmetry_xyhbond_nbd_refined	0.137
r_symmetry_nbtor_other	0.091
r_chiral_restr	0.078
r_symmetry_xyhbond_nbd_other	0.075
r_bond_other_d	0.035
r_metal_ion_refined	0.015
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	20397
Nucleic Acid Atoms
Solvent Atoms	2235
Heterogen Atoms	725

Software

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