#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005 Title: Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the VP8* carbohydrate-binding protein of the human rotavirus strain Wa Authors: Kraschnefski, M.J. / Scott, S.A. / Holloway, G. / Coulson, B.S. / von Itzstein, M. / Blanchard, H.
History
Deposition
Aug 16, 2006
Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0
Apr 3, 2007
Provider: repository / Type: Initial release
Revision 1.1
Apr 1, 2008
Group: Version format compliance
Revision 1.2
Jul 13, 2011
Group: Non-polymer description / Version format compliance
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: 2.5→64.6 Å / Num. obs: 8135
-
Processing
Software
Name
Version
Classification
REFMAC
5.2.0019
refinement
XNEMO
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 porcine CRW-8 VP8* that we have solved. Resolution: 2.5→64.55 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.91 / SU B: 7.301 / SU ML: 0.163 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.402 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23508
355
4.5 %
RANDOM
Rwork
0.17718
-
-
-
obs
0.17973
7491
96.54 %
-
all
-
8114
-
-
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: 31.888 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.36 Å2
0.68 Å2
0 Å2
2-
-
1.36 Å2
0 Å2
3-
-
-
-2.04 Å2
Refinement step
Cycle: LAST / Resolution: 2.5→64.55 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1300
0
20
93
1413
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.008
0.022
1356
X-RAY DIFFRACTION
r_angle_refined_deg
1.106
1.925
1846
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.653
5
161
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.678
24.366
71
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.865
15
209
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
12.765
15
8
X-RAY DIFFRACTION
r_chiral_restr
0.082
0.2
200
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
1057
X-RAY DIFFRACTION
r_nbd_refined
0.197
0.2
583
X-RAY DIFFRACTION
r_nbtor_refined
0.307
0.2
909
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.115
0.2
102
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.206
0.2
40
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.169
0.2
10
X-RAY DIFFRACTION
r_mcbond_it
0.528
1.5
829
X-RAY DIFFRACTION
r_mcangle_it
0.949
2
1322
X-RAY DIFFRACTION
r_scbond_it
1.193
3
608
X-RAY DIFFRACTION
r_scangle_it
1.973
4.5
523
LS refinement shell
Resolution: 2.5→2.565 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.237
23
-
Rwork
0.271
533
-
obs
-
-
97.2 %
+
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