! (Supplementary Information) ! Decrypting Cryptochrome: Revealing the Molecular Identity of the Photoactivation Reaction ! Ilia A. Solov'yov, Tatiana Domratcheva, Abdul Rehaman Moughal Shahi, Klaus Schulten BONDS OH1 CN7 428.000 1.4200 ! ALLOW ALI ALC ARO CN1 CN7 200.000 1.5220 ! ALLOW POL S CN7 240.000 1.8160 ! ALLOW ALI SUL ION CN2 CN7 230.000 1.5100 ! ALLOW ARO !CN2 NN3 450.000 1.3000 !C !CN1 NN2 380.000 1.4100 !C, adm jr. 11/97 !CN1 NN3 350.000 1.3850 !C, adm jr. 11/97 CN7 NN2 270.000 1.3750 ! ALLOW ARO CN1 CN2 302.000 1.4090 !U, adm jr. 11/97 !CN3 CN3 500.000 1.4000 !C,U adm jr. 11/97 !CN2 CN3 320.000 1.4300 CN2 NN2 400.000 1.4000 !G CN2 CN2 302.000 1.4300 !U, adm jr. 11/97 CN3 CN9 230.000 1.4780 !T, adm jr. 11/97 CN1 ON1 660.000 1.2340 !U,A,G par_a4 adm jr. 10/2/91 CN3 HN3 350.000 1.0900 !C,U, JWK ANGLES CN1 NN2 HN2 37.000 121.2 !C, h CN1 NN3 CN2 85.000 119.1 !C CN3 CN2 NN3 85.000 119.3 !C CN2 CN3 HN3 38.000 120.1 !C h5 CN3 CN3 HN3 38.000 122.1 !C,U CN3 CN9 HN9 33.430 110.1 22.53 2.179 ! Alkanes, sacred CN3 CN3 CN9 45.800 122.3 ! ALLOW ALI ARO CN7 CN1 NN2 70.000 116.2 CN1 CN7 NN2 70.000 109.3 CN1 CN7 CN2 70.000 110.9 CN7 CN2 NN3 125.000 121.6 CN7 CN2 NN2 70.000 118.5 CN2 CN1 NN2 70.000 116.0 !6R) CN1 CN2 NN3 125.000 129.0 ! bridgeC5 CN1 NN2 CN1 50.000 125.0 !U CN1 CN2 CN2 70.000 119.6 !6R) bridgeC5 CN2 CN2 NN3 60.000 123.0 !6R) CN2 CN7 NN3 50.000 110.9 CN7 S CT2 34.000 102.4 NN3 CN7 S 44.600 115.6 CN2 CN7 S 21.200 109.1 CN1 CN7 S 19.400 100.5 CN2 CN2 NN2 100.000 116.0 !5R) bridgeC4 CN2 CN1 ON1 50.000 124.7 ! CN7 CN1 ON1 40.000 121.1 CN2 CN2 CN3 60.000 121.0 !6R) bridgeC5 CN2 NN3 CN7 70.000 120.5 CN2 NN3 CN2 90.000 119.4 !6R) CN2 NN2 CN8 70.000 125.9 !9-E-G, adm jr. CN2 NN2 CN2 90.000 122.0 !nad/ppi, jjp1/adm jr. 7/95C CN3 CN2 NN2 100.000 125.7 !5R) bridgeC4 !CN7 CN8 ON2 70.000 108.4 !NF, 11/97, C4'C5'O5' HN7 CN7 OH1 45.900 108.8 ! ALLOW ALI ALC ARO CN7 OH1 H 57.500 106.0 ! ALLOW ALC ARO ALI CN8 CN7 OH1 75.700 110.1 ! ALLOW ALI ALC ARO !CN2 CN3 CN3 85.000 121.3 !FMN CN7 CN7 OH1 75.700 110.1 ! ALLOW ALI ALC ARO CN7 CN7 CN7 53.300 111.0 ! ALLOW ALI CN3 CN3 CN3 40.000 120.0 !35.00 2.41620 ! ALLOW ARO CN7 CN8 NN2 110.000 111.0 !C/A, Arabinose (NF) NN2 CN2 NN3 70.000 122.2 !6R) !NN2 CN1 NN3 50.000 119.5 !C NN2 CN1 ON1 130.000 121.5 !C, o2 NN3 CN1 ON1 130.000 123.8 !C CN2 NN2 CN7 70.000 120.5 CN2 CN7 NN2 70.000 110.8 NN2 CN7 S 44.600 115.6 CN7 NN2 HN2 30.000 118.5 CN2 NN2 HN2 40.000 120.7 DIHEDRALS X CN9 CN3 X 0.0 6 0.0 ! ALLOW ALI ARO X CN7 CN7 X 0.2000 3 0.00 ! ALLOW ALI X CN1 CN2 X 12.0 2 180.0 CN7 CN8 ON2 P 2.5 1 180.0 !eps H OH1 CN7 CN8 1.33 1 0.0 ! ALLOW ALC X CN7 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO X CN2 NN2 X 5.0 2 180.0 ! 1.5 X CN2 CN2 X 6.0 2 180.0 ! !X CN8 CN7 X 0.15 3 0.0 ! Alkanes (0.2 to 0.15) !X CN1 NN2 X 4.0 2 180.0 ! c22 !X CN2 NN3 X 4.0 2 180.0 ! adm jr. 11/97 !X CN1 NN3 X 4.0 2 180.0 ! c22 !X CN2 CN3 X 4.0 2 180.0 ! c22 !X CN3 CN3 X 4.0 2 180.0 ! c22 CN2 NN2 CN8 HN8 0.4 3 0.0 ! 9-E-G CN2 NN2 CN8 CN7 0.6 3 0.0 ! NF ON1 CN1 NN3 CN2 5.0 2 180.0 !for flavin CN9 CN3 CN3 CN2 4.0 2 180.0 !for flavin CN9 CN3 CN3 CN9 4.0 2 180.0 ON1 CN1 NN2 CN1 12.0 2 180.0 !for flavin CN3 CN2 NN3 CN2 8.0 2 180.0 !for flavin HN2 NN2 CN1 ON1 6.0 2 180.0 !for flavin NN3 CN2 CN7 S 2.0 2 83.7 NN3 CN2 CN7 CN1 2.0 2 151.7 NN3 CN2 CN7 NN3 2.0 2 30.0 NN2 CN1 CN7 S 2.0 2 83.7 NN2 CN1 CN7 CN2 2.0 2 -89.4 NN3 CN2 CN7 NN2 3.0 2 -150.0 NN2 CN1 CN7 NN2 3.0 2 150.0 X CN7 S X 0.0 2 0.0 CN1 CN7 CN2 NN2 3.0 2 150.0 CN1 CN7 NN2 CN2 3.0 2 -160.0 ON1 CN1 CN7 S 6.0 2 90.0 ON1 CN1 CN7 CN2 3.0 2 -156.0 ON1 CN1 CN7 NN2 3.0 2 -33.9 CN7 S CT2 CT1 0.2400 1 180.00 ! ALOW ALI SUL ION CN7 S CT2 HA 0.2800 2 0.00 X CN7 CN2 X 3.0 2 150.0 NN2 CN2 CN7 S 3.0 2 -97.9 CN2 NN2 CN7 S 3.0 2 85.7 CN2 NN2 CN7 CN2 3.0 2 -38.8 CN1 CN7 NN2 HN2 2.0 2 25.3 HN2 NN2 CN7 S 2.0 2 -87.6 HN2 NN2 CN7 CN2 2.0 2 147.8 IMPROPER CN3 X X CN3 90.0 0 0.0 !CN1 X X ON1 80.0 0 0.0 CN9 X X CN3 50.0 0 0.0 !T, adm jr. 11/97 CN2 X X CN2 90.0 0 0.0 CN3 X X CN2 90.0 0 0.0 CN2 X X NN3 90.0 0 0.0 CN2 X X NN2 90.0 0 0.0 CN3 X X NN3 90.0 0 0.0 CN3 X X NN2 90.0 0 0.0 ON1 NN3 CN1 NN2 180.0 0 0.0 CN9 CN3 CN3 CN3 120.0 0 0.0 CN1 HN2 NN2 CN1 60.0 0 0.0 ON1 CN2 CN1 NN2 180.0 0 0.0 HN3 CN2 CN3 CN3 60.0 0 0.0 CN3 NN2 CN2 CN2 160.0 0 0.0 CN3 NN3 CN2 CN2 160.0 0 0.0 NN2 NN3 CN2 CN2 160.0 0 0.0 CN1 NN3 CN2 CN2 160.0 0 0.0 NONBONDED CN1 0.0 -0.10 1.9000 CN2 0.0 -0.10 1.9000 CN3 0.0 -0.09 1.9000