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Copy pathDSD_hexFit.txt.
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DSD_hexFit.txt.
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** Showed D3 symmetry mates in crystal structure. saved as PDB
PyMOL>sel /dsd///22-43/
Selector: selection "sele" defined with 990 atoms.
Save: wrote "/home/xray/tertBuilding/dsd_hexamer.pdb".
**Structure Fitter
Structure Summary
selection = "all"
chains 6 (fit 22 residues in each)
chain A 30.770 Å in Z-direction
chain B 30.768 Å in Z-direction; anti-parallel to chain A
chain C 30.770 Å in Z-direction; parallel to chain A
chain D 30.768 Å in Z-direction; anti-parallel to chain A
chain E 30.770 Å in Z-direction; parallel to chain A
chain F 30.768 Å in Z-direction; anti-parallel to chain A
Best-fit Crick parameters[1]:
R0 (Å) 9.425
R1 (Å) 2.289
ω0 (°/res) -1.867
ω1 (°/res) 102.357
α (°) -11.835
φ1 for chain A (°) -74.884
φ1 for chain B (°) -73.701
φ1 for chain C (°) -74.886
φ1 for chain D (°) -73.700
φ1 for chain E (°) -74.887
φ1 for chain F (°) -73.704
Δφ0 for chain B (°) 70.462
Δφ0 for chain C (°) 119.999
Δφ0 for chain D (°) -169.539
Δφ0 for chain E (°) -120.000
Δφ0 for chain F (°) -49.539
starting heptad position for chain A b
starting heptad position for chain B b
starting heptad position for chain C b
starting heptad position for chain D b
starting heptad position for chain E b
starting heptad position for chain F b
pitch (Å) 282.622
rise per residue (Å) 1.498
ΔZoff for chain B (Å) 2.136
ΔZaa' for chain B (Å) 2.159
ΔZoff for chain C (Å) 0.000
ΔZaa' for chain C (Å) 0.000
ΔZoff for chain D (Å) 2.136
ΔZaa' for chain D (Å) 2.159
ΔZoff for chain E (Å) 0.000
ΔZaa' for chain E (Å) 0.000
ΔZoff for chain F (Å) 2.136
ΔZaa' for chain F (Å) 2.159
absolute Zoff for chain B (Å) 0.179
absolute Zoff for chain C (Å) 0.000
absolute Zoff for chain D (Å) 0.179
absolute Zoff for chain E (Å) 0.000
absolute Zoff for chain F (Å) 0.179
RMSD 0.211 Å
processed selection 0f8da3ac0bae.pdb
fit CA trace 0f8da3ac0bae.CA.pdb
fit CA-CA distance 3.83
Full backbone rebuild:
Full backbone PDB file in 0f8da3ac0bae.allbb.pdb
** Sturcutre Generator
Number of chains:
6
Chain length:
22
Coiled-coil parameters
Parameter (symbol, unit) Star End # Samples
Rise per residue (d, Å):
1.51
1.51
constrain1
Superhelical radius (Ro, Å):
10.5
8.4
1000
adjust2 vary
together
Superhelical frequency (ωo, °/aa):
(negative means left-handed superhelix)
-3.5
-1.5
1000
adjust2
Pitch angle (α, °):
-25.14
-8.37
1000
adjust2
α-helical radius (R1, Å):
2.26
2.26
1
α-helical frequency (ω1, °/aa):
102.867
102.867
1
Symmetry (limits variable parameters):
Cn
Dn
Do not impose symmetry
Forcefield minimize final backbone (CA atoms held fixed)
Create a poly-alanine backbone, not a poly-glycine
Chain-wise parameters
Parameter (symbol, unit) Star End Steps
Specify one value for each chain after the first. Separate values with spaces, commas or semicolons. Note that by default, individual chain parameters are traversed independently.
α-helical phase (φ1, °):
-74.884 -73.701 -74.886 -73.700 -74.887 -73.704
-74.884 -73.701 -74.886 -73.700 -74.887 -73.704
1
Superhelical phase offset (Δφ0, °):
70.462 119.999 -169.539 -120.000 -49.539
70.462 119.999 -169.539 -120.000 -49.539
1
Z offset (Zaa', Å):
2.16; 0; 2.16; 0; 2.16
2.16; 0; 2.16; 0; 2.16
1
Orientation versus first chain (p – parallel, ap – antiparallel):
ap; p; ap; p; ap
Couple chain variations
Resulting number of structures (not to exceed 1,000):
1000
http://www.grigoryanlab.org/cccp/output/9bc146fb8baf.html