7ZIP

JC Polyomavirus VP1 in complex with 3'-Sialyllactose glycomacromolecules (aliphatic linker)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4MJ1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1 M HEPES pH 7.5, 0.25 M LiCl, 18% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.734	α = 90
b = 152.505	β = 90
c = 62.952	γ = 90

Symmetry
Space Group	P 21 21 2

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		2022-02-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.99	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	48	99.9	0.13	0.99	13.04	7.42		110486

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	2.01			1.27	0.63

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	4MJ1	1.9	47.963	110486	5525	99.905	0.174	0.1721	0.2155	26.791

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]
1.31			-0.442		-0.869

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.041
r_dihedral_angle_4_deg	22.281
r_dihedral_angle_3_deg	13.5
r_dihedral_angle_1_deg	7.682
r_lrange_it	5.321
r_lrange_other	5.272
r_scangle_it	4.05
r_scangle_other	4.048
r_mcangle_it	3.026
r_mcangle_other	3.026
r_scbond_it	2.718
r_scbond_other	2.717
r_mcbond_it	2.116
r_mcbond_other	2.116
r_angle_refined_deg	1.564
r_angle_other_deg	1.347
r_nbd_other	0.221
r_nbd_refined	0.2
r_symmetry_nbd_other	0.187
r_symmetry_nbd_refined	0.179
r_nbtor_refined	0.16
r_symmetry_xyhbond_nbd_other	0.157
r_xyhbond_nbd_refined	0.148
r_symmetry_xyhbond_nbd_refined	0.133
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.071
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9805
Nucleic Acid Atoms
Solvent Atoms	816
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing