2I2S | pdb_00002i2s

Crystal Structure of the porcine CRW-8 rotavirus VP8* carbohydrate-recognising domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		Homology model based on the structure of Rhesus rotavirus VP8*

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	70% MPD, 0.1M HEPES pH 7.5, methyl-alpha-D-N-acetylneuraminide , VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.929	α = 90
b = 64.663	β = 90
c = 109.886	γ = 90

Symmetry
Space Group	P 21 21 21

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	MAR CCD 165 mm	mirrors	2004-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.9794	ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.3	55.9					17704

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	Homology model based on the structure of Rhesus rotavirus VP8*	2.3	20	17658	16756	901	99.77	0.183	0.1654	0.16256	0.16	0.21952	0.22	RANDOM	21.243

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			1.74		-0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.637
r_dihedral_angle_3_deg	12.934
r_dihedral_angle_4_deg	10.175
r_dihedral_angle_1_deg	6.108
r_scangle_it	1.43
r_angle_refined_deg	1.06
r_scbond_it	0.892
r_mcangle_it	0.593
r_nbtor_refined	0.306
r_mcbond_it	0.306
r_nbd_refined	0.187
r_symmetry_hbond_refined	0.159
r_symmetry_vdw_refined	0.138
r_xyhbond_nbd_refined	0.123
r_metal_ion_refined	0.08
r_chiral_restr	0.063
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2606
Nucleic Acid Atoms
Solvent Atoms	363
Heterogen Atoms	106

Software

Software
Software Name	Purpose
REFMAC	refinement
XNEWMO	data collection
FIP	data collection
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing