The biological unit is a monomer of VP8* which forms part of the rotavirus spike protein (VP4). The spike protein is considered to be formed of a dimer (though some evidence suggests a trimer) of VP4. The crystallographic asymmetric unit contains two molecules of VP8*.
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Components
-
Protein / Sugars , 2 types, 5 molecules AB
#1: Protein
OutercapsidproteinVP4 / spike protein
Mass: 18449.479 Da / Num. of mol.: 2 / Fragment: VP8* domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porcine rotavirus / Species: Rotavirus C / Strain: strain CRW-8 / Plasmid: pGex-VP8*(64-224) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21 DE3 / References: UniProt: P11114, UniProt: P0C6Y8*PLUS
Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 16, 2004 / Details: mirrors
Radiation
Monochromator: silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9794 Å / Relative weight: 1
Reflection
Resolution: 2.3→55.9 Å / Num. obs: 17704
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Processing
Software
Name
Version
Classification
REFMAC
5.2.0019
refinement
XNEWMO
datacollection
FIP
BM30A
datacollection
MOSFLM
datareduction
CCP4
(SCALA)
datascaling
AMoRE
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: Homology model based on the structure of Rhesus rotavirus VP8* Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.307 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.32 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21952
901
5.1 %
RANDOM
Rwork
0.16256
-
-
-
all
0.183
17658
-
-
obs
0.1654
16756
99.77 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 21.243 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1 Å2
0 Å2
0 Å2
2-
-
1.74 Å2
0 Å2
3-
-
-
-0.74 Å2
Refinement step
Cycle: LAST / Resolution: 2.3→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2606
0
106
363
3075
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.007
0.022
2796
X-RAY DIFFRACTION
r_angle_refined_deg
1.06
1.974
3842
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.108
5
324
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.637
24.88
125
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.934
15
413
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
10.175
15
8
X-RAY DIFFRACTION
r_chiral_restr
0.063
0.2
447
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
2098
X-RAY DIFFRACTION
r_nbd_refined
0.187
0.2
1241
X-RAY DIFFRACTION
r_nbtor_refined
0.306
0.2
1926
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.123
0.2
353
X-RAY DIFFRACTION
r_metal_ion_refined
0.08
0.2
6
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.138
0.2
59
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.159
0.2
36
X-RAY DIFFRACTION
r_mcbond_it
0.306
1.5
1633
X-RAY DIFFRACTION
r_mcangle_it
0.593
2
2704
X-RAY DIFFRACTION
r_scbond_it
0.892
3
1217
X-RAY DIFFRACTION
r_scangle_it
1.43
4.5
1138
LS refinement shell
Resolution: 2.3→2.36 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.223
72
-
Rwork
0.178
1212
-
obs
-
-
99.92 %
+
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