7ZIO | pdb_00007zio

JC Polyomavirus VP1 in complex with 6'-Sialyllactose glycomacromolecules (aromatic linker)

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3NXD

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
2.94	58.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 150.02	α = 90
b = 97.258	β = 110.298
c = 129.075	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	1.75	45.165	99.2	0.18	0.99	8.31	5.07		173290

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	1.75	1.86			1.27	0.58

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3NXD	1.751	45.165	173278	3466	99.294	0.184	0.1828	0.2	0.2168	0.23	19.461

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]
0.12		-0.487	1.054		-0.639

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.942
r_dihedral_angle_4_deg	17.262
r_dihedral_angle_3_deg	12.879
r_dihedral_angle_1_deg	7.283
r_lrange_it	5.365
r_lrange_other	4.983
r_scangle_it	3.288
r_scangle_other	3.287
r_scbond_it	2.104
r_scbond_other	2.103
r_mcangle_other	2.02
r_mcangle_it	2.019
r_angle_refined_deg	1.502
r_angle_other_deg	1.38
r_mcbond_it	1.371
r_mcbond_other	1.369
r_nbd_refined	0.2
r_symmetry_nbd_other	0.189
r_xyhbond_nbd_refined	0.189
r_nbd_other	0.18
r_symmetry_xyhbond_nbd_refined	0.171
r_symmetry_xyhbond_nbd_other	0.169
r_nbtor_refined	0.159
r_symmetry_nbd_refined	0.135
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.076
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10058
Nucleic Acid Atoms
Solvent Atoms	1525
Heterogen Atoms	146

Software

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