7ZIQ | pdb_00007ziq

BK Polyomavirus VP1 in complex with 6'-Sialyllactose glycomacromolecules (aromatic 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
2.28	46.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.327	α = 90
b = 151.838	β = 90
c = 63.052	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	48.5	99.9	0.19	0.99	12.84	13.42		110045

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			1.94	0.61

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	4MJ1	1.9	48.5	110045	3302	99.884	0.189	0.1874	0.2	0.2262	0.23	30.528

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]
1.487			0.003		-1.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.367
r_dihedral_angle_4_deg	21.075
r_dihedral_angle_3_deg	13.584
r_dihedral_angle_1_deg	7.441
r_lrange_it	5.893
r_lrange_other	5.892
r_scangle_it	4.552
r_scangle_other	4.552
r_mcangle_it	3.461
r_mcangle_other	3.461
r_scbond_it	3.073
r_scbond_other	3.072
r_mcbond_it	2.417
r_mcbond_other	2.416
r_angle_other_deg	2.384
r_angle_refined_deg	1.492
r_nbd_other	0.28
r_symmetry_xyhbond_nbd_refined	0.237
r_symmetry_nbd_refined	0.222
r_symmetry_nbd_other	0.21
r_nbd_refined	0.199
r_nbtor_refined	0.158
r_xyhbond_nbd_refined	0.154
r_symmetry_xyhbond_nbd_other	0.099
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.066
r_bond_other_d	0.036
r_gen_planes_other	0.01
r_bond_refined_d	0.008
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9838
Nucleic Acid Atoms
Solvent Atoms	748
Heterogen Atoms	108

Software

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