7ZIM

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

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1 M HEPES pH 7.5, 0.2 M KSCN, 12% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 150.146	α = 90
b = 96.635	β = 110.487
c = 128.555	γ = 90

Symmetry
Space Group	C 1 2 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		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	1.55	44.8	95.9	0.1	0.99	10.61	4.74		248912

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	1.55	1.64			1.3	0.49

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	3NXD	1.55	44.8	248910	4979	99.791	0.167	0.167	0.1909	18.833

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]
-0.555		-0.116	-0.02		0.517

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.688
r_dihedral_angle_4_deg	17.539
r_dihedral_angle_3_deg	12.782
r_dihedral_angle_1_deg	7.158
r_lrange_it	5.6
r_lrange_other	5.168
r_scangle_it	3.285
r_scangle_other	3.285
r_angle_other_deg	2.396
r_mcangle_other	2.095
r_mcangle_it	2.094
r_scbond_it	2.072
r_scbond_other	2.072
r_angle_refined_deg	1.502
r_mcbond_it	1.329
r_mcbond_other	1.326
r_symmetry_nbd_other	0.213
r_nbd_refined	0.203
r_nbd_other	0.199
r_xyhbond_nbd_refined	0.173
r_nbtor_refined	0.163
r_symmetry_xyhbond_nbd_refined	0.143
r_symmetry_nbd_refined	0.14
r_symmetry_xyhbond_nbd_other	0.099
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.074
r_bond_other_d	0.036
r_gen_planes_other	0.013
r_bond_refined_d	0.008
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10099
Nucleic Acid Atoms
Solvent Atoms	1703
Heterogen Atoms	110

Software

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