7ZIL | pdb_00007zil

JC Polyomavirus VP1 in complex with 3'-Sialyllactose glycomacromolecules (aliphatic 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% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 150.098	α = 90
b = 96.023	β = 110.555
c = 128.058	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	1.24	48.012	95.9	0.07	0.99	12.14	4.78		464154

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	1.24	1.31			1.04	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3NXD	1.24	48.012	463097	9262	95.983	0.138	0.1375	0.14	0.1547	0.15	16.372

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]
-0.48		0.104	-0.136		0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.985
r_dihedral_angle_4_deg	17.667
r_dihedral_angle_3_deg	12.208
r_rigid_bond_restr	11.366
r_dihedral_angle_1_deg	7.383
r_lrange_it	3.953
r_lrange_other	3.201
r_scangle_it	2.657
r_scangle_other	2.657
r_angle_other_deg	2.476
r_scbond_it	2.195
r_scbond_other	2.195
r_mcangle_it	1.769
r_mcangle_other	1.769
r_angle_refined_deg	1.659
r_mcbond_it	1.423
r_mcbond_other	1.423
r_nbd_refined	0.229
r_symmetry_nbd_other	0.225
r_symmetry_nbd_refined	0.214
r_xyhbond_nbd_refined	0.183
r_nbtor_refined	0.169
r_nbd_other	0.168
r_symmetry_xyhbond_nbd_refined	0.164
r_metal_ion_refined	0.118
r_symmetry_xyhbond_nbd_other	0.103
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.083
r_bond_other_d	0.035
r_gen_planes_other	0.016
r_bond_refined_d	0.011
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10070
Nucleic Acid Atoms
Solvent Atoms	1965
Heterogen Atoms	155

Software

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