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"theta": -169.298, "eta_prime": -170.948, "theta_prime": -164.795, "eta_base": -78.163, "theta_base": 159.343, "v0": -8.884, "v1": 25.760, "v2": -31.758, "v3": 27.515, "v4": -11.881, "amplitude": 31.795, "phase_angle": 182.783, "puckering": "C3'-exo", "sugar_class": "~C2'-endo", "bin": "trig", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.040, "frame": { "rmsd": 0.011, "origin": [ 20.826, -1.820, 4.063 ], "x_axis": [ -0.724, -0.592, -0.354 ], "y_axis": [ 0.397, 0.061, -0.916 ], "z_axis": [ 0.564, -0.804, 0.191 ], "quaternion": [ -0.363, 0.077, -0.631, 0.681 ] } }, { "index": 22, "index_chain": 4, "chain_name": "D", "nt_resnum": 22, "nt_name": "DT", "nt_code": "T", "nt_id": "///D/22", "linked_nts": [ "///D/21", "///D/23" ], "nt_type": "DNA", "dbn": ".", "summary": "anti,~C2'-endo,non-canonical,non-pair-contact,helix,ss-non-loop", "alpha": -68.290, "beta": -172.619, "gamma": 50.666, "delta": 134.768, "epsilon": -112.675, "zeta": null, "epsilon_zeta": null, "bb_type": "--", "chi": 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"dbn": ".", "summary": "non-stack,ss-non-loop", "alpha": null, "beta": null, "gamma": null, "delta": null, "epsilon": null, "zeta": null, "epsilon_zeta": null, "bb_type": "--", "chi": null, "glyco_bond": "--", "C5prime_xyz": [ null, null, null ], "P_xyz": [ null, null, null ], "form": "-", "ssZp": null, "Dp": null, "splay_angle": null, "splay_distance": null, "splay_ratio": null, "d22": null, "d64": null, "eta": null, "theta": null, "eta_prime": null, "theta_prime": null, "eta_base": null, "theta_base": null, "v0": null, "v1": null, "v2": null, "v3": null, "v4": null, "amplitude": null, "phase_angle": null, "puckering": "", "sugar_class": "--", "bin": "inc", "cluster": "__", "suiteness": 0.000, "filter_rmsd": null } ], "num_hbonds": 21, "hbonds": [ { "index": 1, "atom1_serNum": 4, "atom2_serNum": 267, "donAcc_type": "questionable", "distance": 3.343, "atom1_id": "///A/1/O4'", "atom2_id": "///C/14/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 2, "atom1_serNum": 11, "atom2_serNum": 236, "donAcc_type": "standard", "distance": 2.823, "atom1_id": "///A/1/N7", "atom2_id": "///B/12/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 3, "atom1_serNum": 14, "atom2_serNum": 238, "donAcc_type": "standard", "distance": 2.796, "atom1_id": "///A/1/N6", "atom2_id": "///B/12/O4", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 4, "atom1_serNum": 33, "atom2_serNum": 214, "donAcc_type": "standard", "distance": 2.809, "atom1_id": "///A/2/N3", "atom2_id": "///B/11/N7", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 5, "atom1_serNum": 35, "atom2_serNum": 217, "donAcc_type": "standard", "distance": 3.048, "atom1_id": "///A/2/O4", "atom2_id": "///B/11/N6", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 6, "atom1_serNum": 52, "atom2_serNum": 195, "donAcc_type": "standard", "distance": 2.857, "atom1_id": "///A/3/N7", "atom2_id": "///B/10/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 7, "atom1_serNum": 55, "atom2_serNum": 197, "donAcc_type": "standard", "distance": 2.935, "atom1_id": "///A/3/N6", "atom2_id": "///B/10/O4", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 8, "atom1_serNum": 74, "atom2_serNum": 173, "donAcc_type": "standard", "distance": 2.922, "atom1_id": "///A/4/N3", "atom2_id": "///B/9/N7", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 9, "atom1_serNum": 76, "atom2_serNum": 176, "donAcc_type": "standard", "distance": 3.029, "atom1_id": "///A/4/O4", "atom2_id": "///B/9/N6", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 10, "atom1_serNum": 93, "atom2_serNum": 154, "donAcc_type": "standard", "distance": 3.155, "atom1_id": "///A/5/N7", "atom2_id": "///B/8/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 11, "atom1_serNum": 96, "atom2_serNum": 156, "donAcc_type": "standard", "distance": 2.890, "atom1_id": "///A/5/N6", "atom2_id": "///B/8/O4", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 12, "atom1_serNum": 115, "atom2_serNum": 132, "donAcc_type": "standard", "distance": 2.956, "atom1_id": "///A/6/N3", "atom2_id": "///B/7/N7", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 13, "atom1_serNum": 117, "atom2_serNum": 135, "donAcc_type": "standard", "distance": 3.057, "atom1_id": "///A/6/O4", "atom2_id": "///B/7/N6", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 14, "atom1_serNum": 253, "atom2_serNum": 437, "donAcc_type": "standard", "distance": 2.945, "atom1_id": "///C/13/N7", "atom2_id": "///D/22/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 15, "atom1_serNum": 256, "atom2_serNum": 439, "donAcc_type": "standard", "distance": 3.112, "atom1_id": "///C/13/N6", "atom2_id": "///D/22/O4", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 16, "atom1_serNum": 275, "atom2_serNum": 415, "donAcc_type": "standard", "distance": 2.894, "atom1_id": "///C/14/N3", "atom2_id": "///D/21/N7", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 17, "atom1_serNum": 277, "atom2_serNum": 418, "donAcc_type": "standard", "distance": 3.278, "atom1_id": "///C/14/O4", "atom2_id": "///D/21/N6", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 18, "atom1_serNum": 294, "atom2_serNum": 396, "donAcc_type": "standard", "distance": 2.831, "atom1_id": "///C/15/N7", "atom2_id": "///D/20/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 19, "atom1_serNum": 297, "atom2_serNum": 398, "donAcc_type": "standard", "distance": 3.114, "atom1_id": "///C/15/N6", "atom2_id": "///D/20/O4", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 20, "atom1_serNum": 316, "atom2_serNum": 374, "donAcc_type": "standard", "distance": 2.819, "atom1_id": "///C/16/N3", "atom2_id": "///D/19/N7", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 21, "atom1_serNum": 318, "atom2_serNum": 377, "donAcc_type": "standard", "distance": 2.760, "atom1_id": "///C/16/O4", "atom2_id": "///D/19/N6", "atom_pair": "O:N", "residue_pair": "nt:nt" } ], "refCoords": { "purine": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 -0.5000 0.4000", " 3 N -2.2500 -0.5000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 1.2500 5.0000 0.4000", " 6 C 1.2500 -0.5000 0.4000", " 7 C 1.2500 -0.5000 -0.4000", " 8 C 1.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 -0.5000 0.4000", " 11 C -2.2500 -0.5000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ], "pyrimidine": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 1.0000 0.4000", " 3 N -2.2500 1.0000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 1.2500 5.0000 0.4000", " 6 C 1.2500 1.0000 0.4000", " 7 C 1.2500 1.0000 -0.4000", " 8 C 1.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 1.0000 0.4000", " 11 C -2.2500 1.0000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ], "wc_pair": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 -5.0000 0.4000", " 3 N -2.2500 -5.0000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 2.2500 5.0000 0.4000", " 6 C 2.2500 -5.0000 0.4000", " 7 C 2.2500 -5.0000 -0.4000", " 8 C 2.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 -5.0000 0.4000", " 11 C -2.2500 -5.0000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ] }, "metadata": { "license": "http://innovation.columbia.edu/technologies/CU20391", "url": "http://x3dna.org/", "url_alt": "http://home.x3dna.org/", "forum": "http://forum.x3dna.org/", "citation": "Lu et al. (2015). 'DSSR: an integrated software tool for dissecting the spatial structure of RNA.' Nucleic Acids Res., 43(21):e142 [doi:10.1093/nar/gkv716].", "str_id": "1rsb", "num_naChains": 4, "naChains": "A=6,B=6,C=6,D=5", "num_atoms": 476, "num_waters": 34, "num_notes": 52, "notes": [ { "Aminors": "A-minor interactions (including types I and II)" }, { "Cstem_index": "stem index of the 'Canonical' helix in k-turn" }, { "Cstem_pair": "Cstem bp delineating the k-turn internal loop" }, { "Dp": "perpendicular distance of the 3' P atom to the glycosidic bond" }, { "GA_pair": "sheared G-A pair in k-turn" }, { "HtypePknot": "H-type pseudoknot" }, { "Kturn": "kink-turn (k-turn)" }, { "LW": "Leontis-Westhof" }, { "NCstem_index": "stem index of the 'Non-Canonical' helix in k-turn" }, { "NCstem_pair": "NCstem bp delineating the k-turn internal loop" }, { "Uturn": "U-turn of the UNR- or GNRA-type" }, { "aa": "amino acid" }, { "atom_pair": "symbols of the two atoms involved in an H-bond" }, { "auxfiles": "auxiliary files" }, { "glyco_bond": "conformation of base related to sugar (syn or anti)" }, { "bb_type": "backbone conformation, BI or BII" }, { "bending_angle": "angle between two helical axes" }, { "bp": "base pair" }, { "bseq": "base sequence in one-letter code" }, { "bulge": "bulge loop" }, { "coaxStacks": "coaxial stacking of stems within a helix" }, { "dbn": "dot bracket notation" }, { "desc": "description" }, { "donAcc_type": "donor/acceptor type of the atom pair in an H-bond" }, { "epsilon_zeta": "difference between epsilon and zeta torsion angles" }, { "hairpin": "hairpin loop" }, { "hbond": "hydrogen bond (H-bond)" }, { "helix": "defined by base-stacking interactions, regardless of bp type and backbone connectivity" }, { "id": "identifier" }, { "iloop": "internal loop" }, { "index": "serial number" }, { "isoCanonPairs": "isolated canonical pairs" }, { "junction": "(multi-branched) junction loop" }, { "kissingLoop": "kissing loop" }, { "multiplet": "3+ bases in a coplanar geometry" }, { "na": "nucleic acid" }, { "nonPair": "two nts not forming a pair, but with H-bonding/stacking interactions" }, { "nonStack": "nucleotide not involved in stacking interactions" }, { "nt": "nucleotide" }, { "num": "number" }, { "oArea": "overlap areas between two bases, including exocyclic atoms" }, { "oArea_ring": "overlap areas between two bases, including only ring atoms" }, { "phosContacts": "H-bonding and atom-capping interactions involving a phosphate" }, { "residue_pair": "types of the two residues involved in an H-bond" }, { "rmsd": "root-mean-squares deviation" }, { "serNum": "serial number" }, { "ssSegments": "single-stranded segments not involved in loops" }, { "ssZp": "Z-coordinate of the 3' phosphorus atom with reference to the 5' base plane" }, { "sstr": "secondary structure in dbn" }, { "stem": "helix consisting of only canonical pairs, with a continuous backbone" }, { "str_id": "structure identifier, derived from inpfile with extension removed" }, { "vert_dist": "vertical distance from an atom to a base plane" } ], "num_auxfiles": 12, "auxfiles": [ { "index": 1, "name": "dssr-pairs.pdb", "desc": "an ensemble of base pairs" }, { "index": 2, "name": "dssr-helices.pdb", "desc": "an ensemble of helices (coaxial stacking)" }, { "index": 3, "name": "dssr-2ndstrs.bpseq", "desc": "secondary structure in bpseq format" }, { "index": 4, "name": "dssr-2ndstrs.ct", "desc": "secondary structure in connectivity table format" }, { "index": 5, "name": "dssr-2ndstrs.dbn", "desc": "secondary structure in dot-bracket notation" }, { "index": 6, "name": "dssr-torsions.txt", "desc": "backbone torsion angles and suite names" }, { "index": 7, "name": "dssr-splays.pdb", "desc": "an ensemble of splayed-apart units" }, { "index": 8, "name": "dssr-stacks.pdb", "desc": "an ensemble of base stacks" }, { "index": 9, "name": "dssr-rotmat.txt", "desc": "position vector and rotation matrix" }, { "index": 10, "name": "dssr-viewV.pdb", "desc": "vertical view of the principal moment of inertia" }, { "index": 11, "name": "dssr-viewH.pdb", "desc": "horizontal view of the principal moment of inertia" }, { "index": 12, "name": "dssr-viewT.pdb", "desc": "top view of the principal moment of inertia" } ], "time_used": "999" } }