6H9Y | pdb_00006h9y

Unraveling the role of the secretor antigen in human rotavirus attachment to histo-blood group antigens

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6H9W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294.15	1.5M Li2SO4 0.1M Tris pH6.5

Crystal Properties
Matthews coefficient	Solvent content
1.92	35.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.988	α = 90
b = 54.725	β = 97.92
c = 67.433	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2017-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97907	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.31	66.79	94.9	0.087	0.102	0.053	0.995	8.4	3.4		64030

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.31	1.38	97.6		0.6	0.736	0.419	0.739		2.8

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6H9W	1.31	66.79	60807	3204	94.76	0.1821	0.1806	0.19	0.209	0.21	RANDOM	12.386

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]
0.35		-0.42	-0.29		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.796
r_dihedral_angle_4_deg	17.353
r_dihedral_angle_3_deg	13.159
r_dihedral_angle_1_deg	6.26
r_angle_other_deg	3.817
r_angle_refined_deg	2.106
r_chiral_restr	0.155
r_gen_planes_other	0.032
r_bond_refined_d	0.023
r_gen_planes_refined	0.014

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.796
r_dihedral_angle_4_deg	17.353
r_dihedral_angle_3_deg	13.159
r_dihedral_angle_1_deg	6.26
r_angle_other_deg	3.817
r_angle_refined_deg	2.106
r_chiral_restr	0.155
r_gen_planes_other	0.032
r_bond_refined_d	0.023
r_gen_planes_refined	0.014
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2610
Nucleic Acid Atoms
Solvent Atoms	512
Heterogen Atoms	40

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.