#1: Journal: Cell(Cambridge,Mass.) / Year: 2001 Title: The fusion glycoprotein shell of Semliki Forest Virus: an icosahedral assembly primed for fusogenic activation at endosomal pH.
#2: Journal: Nature / Year: 2004 Title: Conformational change and protein-protein interactions of the fusion protein of Semliki Forest virus.
History
Deposition
Aug 5, 2005
Deposition site: RCSB / Processing site: RCSB
Revision 1.0
Jan 17, 2006
Provider: repository / Type: Initial release
Revision 1.1
Apr 30, 2008
Group: Version format compliance
Revision 1.2
Jul 13, 2011
Group: Advisory / Refinement description / Version format compliance
Resolution: 3→3.21 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.124 / Mean I/σ(I) obs: 5.4 / % possible all: 76.1
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 39 Å / Num. measured all: 82854
Reflection shell
*PLUS
Highest resolution: 3 Å / % possible obs: 76.1 %
-
Processing
Software
Name
Version
Classification
REFMAC
5.2.0005
refinement
MOSFLM
datareduction
SCALEPACK
datascaling
MLPHARE
phasing
Refinement
Method to determine structure: MIR / Resolution: 3→39 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.809 / SU B: 52.882 / SU ML: 0.494 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.553 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 8 OF THE SOLVENT MOLECULES ADDED TO POSITIVE FOURIER DIFFERENCE PEAKS (ABOVE 3 SIGMA) ARE FURTHER THAN 3.5 ANGSTROMS AWAY FROM MACROMOLECULE. THE E1 PROTEIN IS GLYCOSYLATED at ASN 141. THE ...Details: 8 OF THE SOLVENT MOLECULES ADDED TO POSITIVE FOURIER DIFFERENCE PEAKS (ABOVE 3 SIGMA) ARE FURTHER THAN 3.5 ANGSTROMS AWAY FROM MACROMOLECULE. THE E1 PROTEIN IS GLYCOSYLATED at ASN 141. THE DENSITY WAS NOT CLEAR ENOUGH TO BUILD A SUGAR AT THIS LOCATION THUS WATER MOLECULES 71 AND 81 WERE PLACED INTO POSITIVE DENSITY NEAR THIS RESIDUE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.31868
1232
10.4 %
RANDOM
Rwork
0.26654
-
-
-
obs
0.27199
10604
87.9 %
-
all
-
13467
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 4.062 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-3.51 Å2
-1.76 Å2
0 Å2
2-
-
-3.51 Å2
0 Å2
3-
-
-
5.27 Å2
Refinement step
Cycle: LAST / Resolution: 3→39 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2935
0
0
88
3023
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.006
0.022
3020
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
2610
X-RAY DIFFRACTION
r_angle_refined_deg
0.996
1.947
4125
X-RAY DIFFRACTION
r_angle_other_deg
0.707
3
6121
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.875
5
383
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.652
24.298
121
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.366
15
466
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
10.636
15
10
X-RAY DIFFRACTION
r_chiral_restr
0.06
0.2
464
X-RAY DIFFRACTION
r_gen_planes_refined
0.002
0.02
3366
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
589
X-RAY DIFFRACTION
r_nbd_refined
0.175
0.2
697
X-RAY DIFFRACTION
r_nbd_other
0.158
0.2
2872
X-RAY DIFFRACTION
r_nbtor_refined
0.173
0.2
1471
X-RAY DIFFRACTION
r_nbtor_other
0.078
0.2
1858
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.153
0.2
113
X-RAY DIFFRACTION
r_xyhbond_nbd_other
0.058
0.2
3
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.124
0.2
14
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.101
0.2
43
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.201
0.2
7
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.184
1.5
2457
X-RAY DIFFRACTION
r_mcbond_other
0.017
1.5
768
X-RAY DIFFRACTION
r_mcangle_it
0.21
2
3129
X-RAY DIFFRACTION
r_scbond_it
0.246
3
1310
X-RAY DIFFRACTION
r_scangle_it
0.378
4.5
996
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 3→3.077 Å / Total num. of bins used: 20
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