1 average structure + 20 structures with the lowest energy
Representative
Model #1
average structure
-
Components
#1: Protein/peptide
Thymosinalpha-1
Mass: 3096.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The protein was made on a protein synthesizer. / Source: (synth.) Homo sapiens (human) / References: UniProt: P06454
Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, andKollm
moleculardynamics
AMBER
9
Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, andKollm
minimization
AMBER
9
Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, andKollm
dataanalysis
AMBER
refinement
Refinement
Method: molecular dynamics, restrained molecular dynamics, restrained molecular dynamics, selection, average structure Software ordinal: 1 Details: 25 ns at 300K on a explicit solvent ratio 40% TFE/H2O (v/v), with a linear-helix initial structure, After the 25 ns on explicit solvent, 1 ns GB simulation follows with all (549)restrains at ...Details: 25 ns at 300K on a explicit solvent ratio 40% TFE/H2O (v/v), with a linear-helix initial structure, After the 25 ns on explicit solvent, 1 ns GB simulation follows with all (549)restrains at 300K., After the 1ns GB restrained simulation, a 10ns restrained MD simulation follows on a explicit solvent ratio 40% TFE/water (v/v). 1000 structures were collected (1 every 10ps), minimized and sorted by total energy. The best 20 structures with the lowest energy were selected., The average structure was obtained from the average of the 20 best structures with the lowest energy and minimized with the 549 restraints and the GB method in order to taking in account the salvation implicitly.
NMR constraints
NOE constraints total: 415 / NOE intraresidue total count: 170 / NOE long range total count: 0 / NOE medium range total count: 106 / NOE sequential total count: 139 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 100 / Protein phi angle constraints total count: 17 / Protein psi angle constraints total count: 17
NMR representative
Selection criteria: average structure
NMR ensemble
Average torsion angle constraint violation: 0.075 ° Conformer selection criteria: 1 average structure + 20 structures with the lowest energy Conformers calculated total number: 1000 / Conformers submitted total number: 21 / Maximum lower distance constraint violation: 0.033 Å / Maximum torsion angle constraint violation: 4.081 ° / Maximum upper distance constraint violation: 0.368 Å Torsion angle constraint violation method: minimizing the sum of the absolute values of the errors
NMR ensemble rms
Distance rms dev: 0.0086 Å / Distance rms dev error: 0.036 Å
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