6Y63

Structure of Sheep Polyomavirus VP1 in complex with 3'-Sialyllactosamine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4FMG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	KSCN, PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.286	α = 90
b = 79.93	β = 116
c = 145.884	γ = 90

Symmetry
Space Group	P 1 21 1

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		2019-11-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.999	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	1.651	48.81	99.82	0.1012	0.999	13.87	6.8		322288

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	1.651	1.71			1.547	0.471	1.22

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	4FMG	1.651	48.807	322280	7413	99.827	0.17	0.1689	0.1999	21.746

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]
-0.433		-0.827	0.814		0.288

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.482
r_dihedral_angle_4_deg	24.253
r_dihedral_angle_3_deg	11.774
r_dihedral_angle_1_deg	7.375
r_lrange_it	4.74
r_lrange_other	4.52
r_scangle_it	2.918
r_scangle_other	2.918
r_mcangle_it	2.135
r_mcangle_other	2.135
r_scbond_it	1.882
r_scbond_other	1.881
r_angle_refined_deg	1.481
r_mcbond_it	1.419
r_mcbond_other	1.418
r_angle_other_deg	1.331
r_symmetry_nbd_refined	0.278
r_nbd_other	0.217
r_symmetry_nbd_other	0.192
r_nbd_refined	0.19
r_nbtor_refined	0.167
r_symmetry_xyhbond_nbd_refined	0.157
r_xyhbond_nbd_refined	0.142
r_symmetry_nbtor_other	0.081
r_symmetry_xyhbond_nbd_other	0.076
r_chiral_restr	0.069
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19601
Nucleic Acid Atoms
Solvent Atoms	2308
Heterogen Atoms	357

Software

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