Kindly provided by Peter S. Klosterman <petek@mail.csb.yale.edu>

The following contains the SHELXL RNA restraint parameters used in refining two RNA structures (ref: Klosterman, Peter S., Shah, Sapan A., and Steitz, Thomas A., Biochemistry 1999, 38, 14784-14792). The parameters are copied from Parkinson, G., Vojtechovsky, J., Clowney, L., Brunger, A.T., and Berman, H.M. (1996) Acta Crystallogr. D52, 57-74, using the law of cosines to translate angle restraints to 1,3 distances. This work represents a joint effort by Peter Klosterman and Joseph Ippolito, also in Tom Steitz's lab.

REM Sugars

DFIX_* 1.485 P O5T
DFIX_* 1.485 P O1P
DFIX_* 1.485 P O2P
DFIX_* 1.593 P O5'
DFIX_* 1.440 O5' C5'
DFIX_* 1.510 C5' C4'
DFIX_* 1.524 C4' C3'
DFIX_* 1.525 C3' C2'
DFIX_* 1.528 C2' C1'
DFIX_* 1.414 O4' C1'
DFIX_* 1.453 O4' C4'
DFIX_* 1.423 O3' C3'
DFIX_* 1.413 O2' C2'

DANG_* 2.567 O5T O1P
DANG_* 2.567 O5T O2P
DANG_* 2.494 O5T O5'
DANG_* 2.567 O1P O2P
DANG_* 2.492 O5' O1P
DANG_* 2.496 O5' O2P
DANG_* 2.420 O5' C4'
DANG_* 2.640 P C5'
DANG_* 2.370 O4' C3'
DANG_* 2.566 C5' C3'
DANG_* 2.415 C5' O4'
DANG_* 2.343 C1' C4'
DANG_* 2.381 C2' C4'
DANG_* 2.364 C3' C1'
DANG_* 2.357 O4' C2'
DANG_* 2.419 C1' O2'
DANG_* 2.455 C3' O2'
DANG_* 2.423 C4' O3'
DANG_* 2.430 C2' O3'

REM Base sugar joint bonds

DFIX_CYT 1.470 C1' N1
DFIX_GUA 1.459 C1' N9
DFIX_URI 1.469 C1' N1
DFIX_ADE 1.462 C1' N9

REM glycosidic bond angles

DANG_GUA 2.327 N9 O4'
DANG_GUA 2.497 N9 C2'
DANG_GUA 2.536 C8 C1'
DANG_GUA 2.531 C4 C1'

DANG_CYT 2.336 N1 O4'
DANG_CYT 2.506 N1 C2'
DANG_CYT 2.467 C6 C1'
DANG_CYT 2.468 C2 C1'

DANG_URI 2.505 N1 C2' ! 1.469 1.528 113.400
DANG_URI 2.336 N1 O4' ! 1.469 1.414 108.200
DANG_URI 2.478 C6 C1' ! 1.469 1.375 121.200
DANG_URI 2.440 C2 C1' ! 1.469 1.381 117.700

DANG_ADE 2.499 N9 C2' ! 1.462 1.528 113.400
DANG_ADE 2.330 N9 O4' ! 1.462 1.414 108.200
DANG_ADE 2.545 C8 C1' ! 1.462 1.373 127.700
DANG_ADE 2.531 C4 C1' ! 1.462 1.374 126.300

REM Phosphate Linkages

DFIX_* 1.607 O3'_- P
DANG_* 2.622 C3'_- P
DANG_* 2.493 O3'_- O1P
DANG_* 2.507 O3'_- O2P
DANG_* 2.522 O3'_- O5'

REM Cytosine

DFIX_CYT 1.240 C2 O2
DFIX_CYT 1.335 C4 N4
DFIX_CYT 1.397 C2 N1
DFIX_CYT 1.367 C6 N1
DFIX_CYT 1.353 C2 N3
DFIX_CYT 1.335 C4 N3
DFIX_CYT 1.425 C4 C5
DFIX_CYT 1.339 C6 C5

DANG_CYT 2.397 C6 C2
DANG_CYT 2.372 N1 N3
DANG_CYT 2.327 C2 C4
DANG_CYT 2.413 N3 C5
DANG_CYT 2.362 C4 C6
DANG_CYT 2.355 C5 N1
DANG_CYT 2.272 O2 N1
DANG_CYT 2.267 O2 N3
DANG_CYT 2.289 N4 N3
DANG_CYT 2.393 C5 N4

REM Guanine

DFIX_GUA 1.373 N1 C2
DFIX_GUA 1.323 N3 C2
DFIX_GUA 1.350 N3 C4
DFIX_GUA 1.379 C5 C4
DFIX_GUA 1.419 C5 C6
DFIX_GUA 1.391 N1 C6
DFIX_GUA 1.388 N7 C5
DFIX_GUA 1.305 N7 C8
DFIX_GUA 1.374 N9 C8
DFIX_GUA 1.375 N9 C4
DFIX_GUA 1.341 N2 C2
DFIX_GUA 1.237 C6 O6

DANG_GUA 2.453 C6 C2
DANG_GUA 2.379 N1 N3
DANG_GUA 2.215 C2 C4
DANG_GUA 2.459 N3 C5
DANG_GUA 2.408 C4 C6
DANG_GUA 2.323 C5 N1
DANG_GUA 2.278 C4 N7
DANG_GUA 2.127 C5 C8
DANG_GUA 2.236 N7 N9
DANG_GUA 2.201 C8 C4
DANG_GUA 2.191 N9 C5
DANG_GUA 2.428 N3 N9
DANG_GUA 2.548 C6 N7
DANG_GUA 2.304 N1 N2
DANG_GUA 2.306 N3 N2
DANG_GUA 2.276 N1 O6
DANG_GUA 2.395 C5 O6

REM Uracil

DFIX_URI 1.219 C2 O2
DFIX_URI 1.232 C4 O4
DFIX_URI 1.381 N1 C2
DFIX_URI 1.375 N1 C6
DFIX_URI 1.373 C2 N3
DFIX_URI 1.380 N3 C4
DFIX_URI 1.431 C4 C5
DFIX_URI 1.337 C5 C6

DANG_URI 2.399 C6 C2 ! 1.375 1.381 121.000
DANG_URI 2.321 N1 N3 ! 1.381 1.373 114.900
DANG_URI 2.464 C2 C4 ! 1.373 1.380 127.000
DANG_URI 2.366 N3 C5 ! 1.380 1.431 114.600
DANG_URI 2.394 C4 C6 ! 1.431 1.337 119.700
DANG_URI 2.380 C5 N1 ! 1.337 1.375 122.700
DANG_URI 2.284 N1 O2 ! 1.381 1.219 122.800
DANG_URI 2.270 N3 O2 ! 1.373 1.219 122.200
DANG_URI 2.256 N3 O4 ! 1.380 1.232 119.400
DANG_URI 2.373 C5 O4 ! 1.431 1.232 125.900

REM Adenine

DFIX_ADE 1.339 N1 C2
DFIX_ADE 1.331 C2 N3
DFIX_ADE 1.344 N3 C4
DFIX_ADE 1.383 C4 C5
DFIX_ADE 1.406 C5 C6
DFIX_ADE 1.351 C6 N1
DFIX_ADE 1.388 C5 N7
DFIX_ADE 1.311 N7 C8
DFIX_ADE 1.373 C8 N9
DFIX_ADE 1.374 N9 C4
DFIX_ADE 1.335 C6 N6

DANG_ADE 2.313 C6 C2 ! 1.351 1.339 118.600
DANG_ADE 2.413 N1 N3 ! 1.339 1.331 129.300
DANG_ADE 2.199 C2 C4 ! 1.331 1.344 110.600
DANG_ADE 2.438 N3 C5 ! 1.344 1.383 126.800
DANG_ADE 2.378 C4 C6 ! 1.383 1.406 117.000
DANG_ADE 2.358 C5 N1 ! 1.406 1.351 117.700
DANG_ADE 2.279 C4 N7 ! 1.383 1.388 110.700
DANG_ADE 2.126 C5 C8 ! 1.388 1.311 103.900
DANG_ADE 2.191 C8 C4 ! 1.373 1.374 105.800
DANG_ADE 2.199 N9 C5 ! 1.374 1.383 105.800
DANG_ADE 2.437 N3 N9 ! 1.344 1.374 127.400
DANG_ADE 2.555 C6 N7 ! 1.406 1.388 132.300
DANG_ADE 2.310 N1 N6 ! 1.351 1.335 118.600
DANG_ADE 2.417 C5 N6 ! 1.406 1.335 123.700
DANG_ADE 2.249 N7 N9 ! 1.311 1.373 113.800

REM Base Planarity Constraints

FLAT_ADE C1' N1 C2 N3 C4 C5 C6 N6 N7 C8 N9
FLAT_GUA C1' N1 C2 N2 N3 C4 C5 C6 O6 N7 C8 N9
FLAT_URI C1' N1 C2 O2 N3 C4 O4 C5 C6
FLAT_CYT C1' N1 C2 O2 N3 C4 N4 C5 C6

END