WAXS in Solvent (WAXSiS) computes small- and wide-angle X-ray scattering curves based on explicit-solvent all-atom molecular dynamics simulations.

Results for job sample

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  • PDB ID entered: 1LYS
  • Biounit: 1
  • Heavy Atoms: 1099
  • q scattering vector: 1.00
  • Number of q values: 101
  • Solvent Density: 334 e/nm-3
  • Envelope Distance: 7 Å
  • Ligands: Keep ligands, try to remove crystallization agents
  • Buffer Subtraction: Total buffer scattering subtracted
  • Selenomethionine: Replaced with methionine
  • Output q Units: Å-1
  • Convergence: Normal
  • Random Seed for Initial Velocities: No



Removed 14 crystal water with a distance > 0.4nm from the protein

MD simulation:
	Estimate for number of atoms in envelope = 5988 - will generate 247 simulation frames
	Simulation time (ps)    = 129.5
	Equilibration time (ps) = 6
	Simulation system contained 1968 solute atoms and 8604 water molecules.
	Solute has zero charge - no counter ions required.

SAXS/WAXS calculation:
	Maximum q scattering vector [nm-1]:                   10
	Number of solute and pure-sovlent simulation frames:  247
	Simulation time discarded for equilibration (ps):     6
	Correcting solvent density to [e/nm3]:                334
	Number of q-points for spherical average:             Max{500, 0.20*(D*q)^2}  [D = diameter of envelope]
	Distance of envelope from solute [nm]:                0.7
	Maximum diameter of solute [nm]:                      4.89634
	Number of atoms used for rotational fit:              387
	Buffer subtraction scheme:                            Total buffer intensity subtracted

Guinier fit:
	Rg [A] = 14.9012
	For comparison: Rg(solute) [A] = 14.1918



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