6VKX | pdb_00006vkx

Crystal structure of the carbohydrate-binding domain VP8* of human P[8] rotavirus strain BM13851

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	295	0.1 M HEPES sodium pH 7.5, 2% v/v PEG 400, 2.0 M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.999	α = 90
b = 63.248	β = 90.7
c = 71.941	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	100	CCD	RAYONIX MX-225		2019-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97931	APS	31-ID

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	1.71	56	90	0.055	0.065	0.035	0.998	12.7	3.3		48913

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	1.71	1.8	97.4		0.464	0.551	0.294	0.799		3.4

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6NIW	1.71	32.17	46518	2380	89.83	0.1993	0.1978	0.228	RANDOM	21.764

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]
-0.98		-0.4	0.09		0.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.379
r_dihedral_angle_4_deg	13.898
r_dihedral_angle_3_deg	12.353
r_dihedral_angle_1_deg	7.801
r_angle_other_deg	1.355
r_angle_refined_deg	1.321
r_chiral_restr	0.062
r_gen_planes_refined	0.013
r_bond_refined_d	0.008
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.379
r_dihedral_angle_4_deg	13.898
r_dihedral_angle_3_deg	12.353
r_dihedral_angle_1_deg	7.801
r_angle_other_deg	1.355
r_angle_refined_deg	1.321
r_chiral_restr	0.062
r_gen_planes_refined	0.013
r_bond_refined_d	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3812
Nucleic Acid Atoms
Solvent Atoms	117
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
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.