Content:
A range of structures were selected from the pdb encompassing a range of resolution, ligand size and complexity.
Rather than directly using the 2Fo-Fc density map from the refined model the following procedure was adopted:
refine -p molrep.pdb -m data.mtz -autoncs -d FIRST FitMAP -p FIRST/refine.pdb -m FIRST/2Fo-Fc.map -dm FIRST/Fo-Fc.map refine -p protein_fitted.pdb -m data.mtz -autoncs -L -d SECOND
This results in water insertion being applied during refinement. Before the final cycle likely areas for ligand binding are found and the model water molecules in this area are removed from the model, but kept for the purposes of defining the bulk solvent mask. This is found to improve difference density.
rhofit -lp ideal.pdb -m refine.mtz -p refine.pdb -d RHOFIT
PDB code | ligand code | Correct solution No. & (CC) | rhofit ligand rms disp to pdb position | picture (1) |
2jdo | I5S | 1 (0.8898) | 0.24 | |
2jdr | L20 | 1 (0.8719) | 0.47 | |
2jds | L20 | 1 (0.8452) | 0.34 | |
2jdt | I5S | 1 (0.8903) | 0.40 | |
2jdv | L20 | 1 (0.9046) | 0.12 | |
1w0f(2) | HEM | 1 (0.8217) | 0.43 | |
1w0f(2) | STR | 1 (0.8633) | 0.51 | |
1w0g | MYT | 2 (0.7766) | 1.20 | |
2w1i(3) | L0I | 1 (0.8200) | 0.61 | |
2vin(4) | 505 | 1 (0.6942) | 0.17 | |
2vio | L10 | 1 (0.8328) | 0.19 | |
2vip(5) | L1R | 1 (0.8235) & 2 (0.8198) | 0.27 & 0.46 | |
2viq(6) | D55 | 1 (0.7606) | 0.65 | |
2viv | VG2 | 1 (0.7775) | 1.39 | |
2jjc | LGA | 3 (0.7176) | 0.08 | |
3gnv | XNZ | 1 (0.9187) | 0.35 | |
3gnw(7) | XNC | 1 (0.8327) : 1 (0.8909) | 0.90 : 0.32 | |
3h98 | B5P | 1 (0.8978) | 0.45 | |
3e51 | N35 | 1 (0.8778) | 0.74 | |
3gol | XND | 1 (0.8990) | 0.25 | |
3d28 | B34 | 1 (0.8736) | 0.25 | |
3i3k(8) | BCD | 1 (0.8402)A & 1 (0.8047)B | 0.83 & 1.08 | |
3i3k(8) | KLN | 1 (0.8939)A & 8 (0.8656)B | 0.38 & 0.52 | |
2zym | ACX | 1 (0.8397) | 0.38 | |
2zyn | BCD | 1 (0.8255) | 0.27 | |
2v8l | BCD | 1 (0.8081) | 0.43 |
Out of 24 tests, the correct answer was found in ALL cases and as the top solution in all but 3 cases.
Page by Andrew Sharff 11 November 2009. Address problems, corrections and clarifications to buster-develop@globalphasing.com