7B6U

Sheep Polyomavirus VP1 in complex with 5 mM Forssman antigen pentaose and 20 mM 6'-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
3.5	64.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.645	α = 90
b = 129.645	β = 90
c = 220.431	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	1.9	49.48	99.8	0.1461	0.996	9.46	5.3		325151			31.3

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	1.9	2.02			1.223	0.441	1.33

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	1.901	49.47	321986	3164	99.764	0.1461	0.1461	0.1726	26.683

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]
-5.055			-5.055		10.111

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.104
r_dihedral_angle_4_deg	22.319
r_dihedral_angle_3_deg	12.507
r_dihedral_angle_1_deg	7.94
r_lrange_it	4.796
r_lrange_other	4.687
r_scangle_it	3.338
r_scangle_other	3.338
r_mcangle_other	2.892
r_mcangle_it	2.891
r_angle_other_deg	2.744
r_scbond_it	2.42
r_scbond_other	2.42
r_mcbond_it	2.124
r_mcbond_other	2.123
r_angle_refined_deg	1.65
r_nbd_other	0.271
r_symmetry_nbd_other	0.217
r_symmetry_xyhbond_nbd_refined	0.184
r_symmetry_nbd_refined	0.179
r_nbd_refined	0.178
r_nbtor_refined	0.166
r_xyhbond_nbd_refined	0.15
r_symmetry_xyhbond_nbd_other	0.134
r_symmetry_nbtor_other	0.096
r_chiral_restr	0.079
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	20381
Nucleic Acid Atoms
Solvent Atoms	2023
Heterogen Atoms	893

Software

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