Experiment: 6VU6

Sialic acid binding region of Streptococcus Sanguinis SK1 adhesin bound to 3'sLn

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6VS7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.6	298	Protein concentration: 72 mg/mL, Protein buffer: 150 mM NaCl, 20 mM tris pH 7.6, Reservoir solution: 20% (w/v) PEG 3350, 0.2 M MgSO4, 0.01 M SrCl2. Crystals were soaked with 10mM 3'-sialyl-N-acetyllactosamine, 20% (w/v) PEG 3350, 0.2 M MgSO4, 0.01 M SrCl2. Cryoprotectant: 40% (1:1 ethylene glycol:glycerol) and 60% reservoir solution

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.213	α = 90
b = 269.859	β = 90
c = 47.511	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	100	CCD	RAYONIX MX-300		2017-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.9795	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	2.1	50	92.37	0.086	16.264	4.3		55942			32.29

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.18			0.727

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6VS7	2.1	35.1	1.34	55880	2751	87.37	0.2257	0.2245	0.2258	0.2477	0.2492	36.93

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	22.2327
f_angle_d	1.7837
f_chiral_restr	0.1157
f_bond_d	0.0184
f_plane_restr	0.0093

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6272
Nucleic Acid Atoms
Solvent Atoms	317
Heterogen Atoms	192

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing