REM ================================================ REM DNA Dictionary for SHELXL REM Revised 11/7/99 by Chad C. Sines REM Lit: REM Sugar/Base Restraints: REM L. Clowney et al., Geometric Parameters in Nucleic REM Acids: Nitrogenous Bases, REM J. Am. Chem. Soc. (1996) 118, 509-518 REM REM A. Gelbin et al., Geometric Parameters in Nucleic REM Acids: Sugar and Phosphate Constituents, REM J. Am. Chem. Soc. (1996) 118, 519-529 REM REM G. Parkinson et al., New Parameters for the Refinement REM of Nucleic Acid-Containing Structures, REM Acta Cryst. (1996) D52, 57-64 REM http://ndbserver.rutgers.edu:80/ REM REM Spermine Restraints: REM Y. Iitaka et al., Acta Cryst. (1965) 18, 110-121. REM REM ================================================ REM Similar chiral volume restraints on deoxyriboses REM ================================================ CHIV_* C1' 2.44 0.03 CHIV_* C3' -2.54 0.03 CHIV_* C4' -2.49 0.03 REM ================================================ REM Planarity restraints for bases (REM if not needed here) REM ================================================ FLAT_C C1' O2 N4 N1 C2 N3 C4 C5 C6 FLAT_T C1' O2 O4 N1 C2 N3 C4 C5 C6 C5M FLAT_A C1' C2 N6 N1 N3 C4 C5 C6 N7 C8 N9 FLAT_G C1' N2 O6 N1 C2 N3 C4 C5 C6 N7 C8 N9 REM ================================================ REM Adding Hydrogens REM Remove REM to generate hydrogen atoms. Note OH for first O5' and REM last O3' - the latter residue number will have to be changed for REM other structures. All hydrogens have been included although using REM all may not be justified REM ================================================ !SUGAR TERMINAL HYDROXYLS REM HFIX_1 87 O5' REM HFIX_13 87 O5' REM HFIX_12 87 O3' REM HFIX_24 87 O3' !SUGAR HYDROGENS REM HFIX_* 13 C1' C3' C4' !safe hydrogen REM HFIX_* 23 C2' C5' !safe hydrogen !BASE HYDROGENS REM HFIX_C 43 C5 C6 !safe hydrogen REM HFIX_C 93 N4 REM HFIX_T 43 N3 C6 !safe hydrogen REM HFIX_T 33 C5M REM HFIX_A 43 C2 C8 !safe hydrogen REM HFIX_A 93 N6 REM HFIX_G 43 N1 C8 !safe hydrogen REM HFIX_G 93 N2 REM REM @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ REM @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ REM Both C2' and C3' Endo sugar restraints have been included. REM You may REM out all the restraints for the conformation that REM is not applicable or you may "mix-and-match" conformations by REM specifying residue numbers. Certain phosphate restraints are REM conformation dependent and have been marked REM @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ REM @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ REM REM ================================================ REM Sugar Restraints- REM C3' ENDO. REM ================================================ REM DFIX_* 1.519 C1' C2' REM DFIX_* 1.518 C2' C3' REM DFIX_* 1.521 C3' C4' REM DFIX_* 1.449 C4' O4' REM DFIX_* 1.418 O4' C1' REM DFIX_* 1.419 C3' O3' REM DFIX_* 1.509 C5' C4' REM DFIX_G 1.488 C1' N9 REM DFIX_A 1.488 C1' N9 REM DFIX_C 1.488 C1' N1 REM DFIX_T 1.488 C1' N1 REM DFIX_* 1.423 O5' C5' REM DANG_* 2.367 C1' C3' REM DANG_* 2.365 C2' C4' REM DANG_* 2.349 C3' O4' REM DANG_* 2.353 C4' C1' REM DANG_* 2.359 O4' C2' REM DANG_* 2.444 C2' O3' REM DANG_* 2.442 C4' O3' REM DANG_* 2.565 C5' C3' REM DANG_* 2.420 C5' O4' REM DANG_A 2.356 O4' N9 REM DANG_G 2.356 O4' N9 REM DANG_C 2.356 O4' N1 REM DANG_T 2.356 O4' N1 REM DANG_A 2.502 C2' N9 REM DANG_G 2.502 C2' N9 REM DANG_C 2.502 C2' N1 REM DANG_T 2.502 C2' N1 REM DANG_* 2.417 O5' C4' REM DANG_A 2.526 C1' C4 REM DANG_G 2.527 C1' C4 REM DANG_C 2.467 C1' C2 REM DANG_T 2.449 C1' C2 REM ================================================ REM Phosphate Restraints for C3' endo(first P is in residue 2). REM Note P-O-C angles more flexible than other angles. REM ================================================ REM DFIX_* 1.485 O1P P O2P P REM DFIX_* 1.607 O3' P_+ REM DFIX_* 1.593 O5' P REM DFIX_* 1.440 O5' C5' REM DFIX_* 1.433 O3' C3' REM DANG_* 2.567 O1P O2P REM DANG_* 2.454 O5' O1P O5' O2P ! SMALL REM DANG_* 2.533 O5' O1P O5' O2P ! LARGE REM DANG_* 2.522 O3' O5'_+ REM DANG_* 2.640 P C5' REM DANG_* 2.630 C3' P_+ REM DANG_* 2.457 O3' O1P_+ O3' O2P_+ ! SMALL REM DANG_* 2.541 O3' O1P_+ O3' O2P_+ ! LARGE REM DANG_* 2.407 O5' C4' !conformation dependent REM DANG_* 2.410 O3' C4' !conformation dependent REM @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ REM ================================================ REM Sugar Restraints- REM C2' ENDO. REM ================================================ DFIX_* 1.518 C1' C2' DFIX_* 1.516 C2' C3' DFIX_* 1.529 C3' C4' DFIX_* 1.446 C4' O4' DFIX_* 1.420 O4' C1' DFIX_* 1.435 C3' O3' DFIX_* 1.512 C5' C4' DFIX_G 1.468 C1' N9 DFIX_A 1.468 C1' N9 DFIX_C 1.468 C1' N1 DFIX_T 1.468 C1' N1 DFIX_* 1.424 O5' C5' DANG_* 2.366 C1' C3' DANG_* 2.385 C2' C4' DANG_* 2.376 C3' O4' DANG_* 2.349 C4' C1' DANG_* 2.346 O4' C2' DANG_* 2.409 C2' O3' DANG_* 2.424 C4' O3' DANG_* 2.552 C5' C3' DANG_* 2.413 C5' O4' DANG_A 2.337 O4' N9 DANG_G 2.337 O4' N9 DANG_C 2.337 O4' N1 DANG_T 2.337 O4' N1 DANG_A 2.509 C2' N9 DANG_G 2.509 C2' N9 DANG_C 2.509 C2' N1 DANG_T 2.509 C2' N1 DANG_* 2.414 O5' C4' DANG_A 2.536 C1' C4 DANG_G 2.537 C1' C4 DANG_C 2.453 C1' C2 DANG_T 2.436 C1' C2 REM ================================================ REM Phosphate Restraints for C2' endo(first P is in residue 2). REM Note P-O-C angles more flexible than other angles. REM ================================================ DFIX_* 1.485 O1P P O2P P DFIX_* 1.607 O3' P_+ DFIX_* 1.593 O5' P DFIX_* 1.440 O5' C5' DFIX_* 1.433 O3' C3' DANG_* 2.567 O1P O2P DANG_* 2.454 O5' O1P O5' O2P ! SMALL DANG_* 2.533 O5' O1P O5' O2P ! LARGE DANG_* 2.522 O3' O5'_+ DANG_* 2.640 P C5' DANG_* 2.630 C3' P_+ DANG_* 2.457 O3' O1P_+ O3' O2P_+ ! SMALL DANG_* 2.541 O3' O1P_+ O3' O2P_+ ! LARGE DANG_* 2.410 O5' C4' !conformation dependent DANG_* 2.416 O3' C4' !conformation dependent REM ================================================ REM Cytosine REM ================= REM 1-2 Distances DFIX_C 1.397 N1 C2 DFIX_C 1.367 N1 C6 DFIX_C 1.353 C2 N3 DFIX_C 1.240 C2 O2 DFIX_C 1.335 N3 C4 DFIX_C 1.425 C4 C5 DFIX_C 1.335 C4 N4 DFIX_C 1.339 C5 C6 REM ----------------------- REM 1-3 Distances REM ----------------------- DANG_C 2.397 C6 C2 DANG_C 2.372 N1 N3 DANG_C 2.329 C2 C4 DANG_C 2.413 N3 C5 DANG_C 2.362 C4 C6 DANG_C 2.355 C5 N1 DANG_C 2.272 N1 O2 DANG_C 2.267 N3 O2 DANG_C 2.289 N3 N4 DANG_C 2.393 C5 N4 DANG_C 2.467 C6 C1' DANG_C 2.468 C2 C1' REM ================================================ REM Thymine REM ================ REM 1-2 Distances DFIX_T 1.376 N1 C2 DFIX_T 1.378 N1 C6 DFIX_T 1.373 C2 N3 DFIX_T 1.220 C2 O2 DFIX_T 1.382 N3 C4 DFIX_T 1.445 C4 C5 DFIX_T 1.228 C4 O4 DFIX_T 1.339 C5 C6 DFIX_T 1.496 C5 C5M REM ----------------------- REM 1-3 Distances REM ----------------------- DANG_T 2.401 C2 C6 DANG_T 2.313 N1 N3 DANG_T 2.468 C2 C4 DANG_T 2.387 N3 C5 DANG_T 2.387 C4 C6 DANG_T 2.396 N1 C5 DANG_T 2.284 N1 O2 DANG_T 2.272 N3 O2 DANG_T 2.261 N3 O4 DANG_T 2.372 O4 C5 DANG_T 2.534 C4 C5M DANG_T 2.491 C6 C5M DANG_T 2.474 C6 C1' DANG_T 2.445 C2 C1' REM ================================================ REM Adenine REM ================ REM 1-2 Distances DFIX_A 1.339 N1 C2 DFIX_A 1.351 N1 C6 DFIX_A 1.331 C2 N3 DFIX_A 1.344 N3 C4 DFIX_A 1.383 C4 C5 DFIX_A 1.406 C5 C6 DFIX_A 1.335 N6 C6 DFIX_A 1.374 C4 N9 DFIX_A 1.373 C8 N9 DFIX_A 1.311 N7 C8 DFIX_A 1.388 N7 C5 REM ----------------------- REM 1-3 Distances REM ----------------------- DANG_A 2.313 C6 C2 DANG_A 2.413 N1 N3 DANG_A 2.199 C2 C4 DANG_A 2.438 N3 C5 DANG_A 2.378 C4 C6 DANG_A 2.360 C5 N1 DANG_A 2.280 C4 N7 DANG_A 2.126 C5 C8 DANG_A 2.249 N7 N9 DANG_A 2.191 C8 C4 DANG_A 2.199 N9 C5 DANG_A 2.437 N3 N9 DANG_A 2.555 C6 N7 DANG_A 2.310 N1 N6 DANG_A 2.417 C5 N6 DANG_A 2.545 C8 C1' DANG_A 2.531 C4 C1' REM ================================================ REM Guanine REM ================ REM 1-2 Distances DFIX_G 1.373 N1 C2 DFIX_G 1.391 N1 C6 DFIX_G 1.341 C2 N2 DFIX_G 1.323 C2 N3 DFIX_G 1.350 N3 C4 DFIX_G 1.379 C4 C5 DFIX_G 1.375 C4 N9 DFIX_G 1.419 C5 C6 DFIX_G 1.388 C5 N7 DFIX_G 1.237 C6 O6 DFIX_G 1.305 N7 C8 DFIX_G 1.374 C8 N9 REM ----------------------- REM 1-3 Distances REM ----------------------- DANG_G 2.453 C6 C2 DANG_G 2.379 N1 N3 DANG_G 2.215 C2 C4 DANG_G 2.459 N3 C5 DANG_G 2.408 C4 C6 DANG_G 2.323 C5 N1 DANG_G 2.278 C4 N7 DANG_G 2.127 C5 C8 DANG_G 2.236 N7 N9 DANG_G 2.201 C8 C4 DANG_G 2.191 N9 C5 DANG_G 2.428 N3 N9 DANG_G 2.548 C6 N7 DANG_G 2.304 N1 N2 DANG_G 2.306 N3 N2 DANG_G 2.276 N1 O6 DANG_G 2.395 C5 O6 DANG_G 2.563 C8 C1' DANG_G 2.531 C4 C1' REM ================================================ REM ====== ADDITIONAL RESIDUES ====== REM ================================================ REM @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ REM Spermine restraints REM ================ REM 1-2 Distances REM ---------------------- REM DFIX_SPM 1.500 N1 C2 REM DFIX_SPM 1.510 C2 C3 REM DFIX_SPM 1.520 C3 C4 REM DFIX_SPM 1.510 C6 C7 REM DFIX_SPM 1.540 C7 C8 REM DFIX_SPM 1.510 C4 N5 REM DFIX_SPM 1.490 N5 C6 REM DFIX_SPM 1.540 C7 C8 REM DFIX_SPM 1.490 C9 N10 REM DFIX_SPM 1.51 N10 C11 REM DFIX_SPM 1.52 C11 C12 REM DFIX_SPM 1.51 C12 C13 REM DFIX_SPM 1.50 C13 N14 REM ----------------------- REM 1-3 Distances REM ---------------------- REM DANG_SPM 2.495 N1 C3 REM DANG_SPM 2.467 C2 C4 REM DANG_SPM 2.512 C3 N5 REM DANG_SPM 2.472 C4 C6 REM DANG_SPM 2.487 N5 C7 REM DANG_SPM 2.514 C6 C8 REM DANG_SPM 2.514 C6 C8 REM DANG_SPM 2.487 C8 N10 REM DANG_SPM 2.472 C9 C11 REM DANG_SPM 2.512 N10 C12 REM DANG_SPM 2.467 C11 C13 REM DANG_SPM 2.495 C12 N14 REM ================================================ REM Hydrated Magnessium REM ==================== REM 1-2 Distances DFIX_ION 2.125 MG O1 MG O2 MG O3 MG O4 MG O5 MG O6 REM ====================== REM 1-3 Distances REM ---------------- DANG_ION 4.250 O1 O3 O5 O6 O2 O4 DANG_ION 3.005 O1 O6 O1 O4 O1 O5 O1 O2 O4 O5 O4 O6 DANG_ION 3.005 O3 O4 O3 O6 O3 O2 O3 O5 O2 O6 O2 O5 REM Dictionary END REM @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@