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"splay_distance": 3.152, "splay_ratio": 0.164, "d22": null, "d64": null, "eta": -168.381, "theta": -127.263, "eta_prime": -150.764, "theta_prime": -128.138, "eta_base": -123.350, "theta_base": -100.123, "v0": -1.540, "v1": -23.486, "v2": 38.304, "v3": -40.143, "v4": 26.064, "amplitude": 40.915, "phase_angle": 20.579, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.699, "filter_rmsd": 0.104, "frame": { "rmsd": 0.014, "origin": [ 9.617, 12.344, 32.575 ], "x_axis": [ 0.970, -0.244, 0.012 ], "y_axis": [ 0.008, -0.020, -1.000 ], "z_axis": [ 0.244, 0.970, -0.018 ], "quaternion": [ 0.695, -0.708, 0.083, -0.090 ] } }, { "index": 20, "index_chain": 10, "chain_name": "B", "nt_resnum": 20, "nt_name": "DG", "nt_code": "G", "nt_id": "///B/20", "linked_nts": [ "///B/19", null ], "nt_type": "DNA", "dbn": ")", "summary": "anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end", "alpha": -146.342, "beta": 168.365, "gamma": 67.107, "delta": 127.389, "epsilon": null, "zeta": null, "epsilon_zeta": null, "bb_type": "--", "chi": -104.288, "glyco_bond": "anti", "C5prime_xyz": [ -3.072, 7.967, -2.210 ], "P_xyz": [ -0.807, 8.738, -3.224 ], "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": -35.187, "v1": 36.245, "v2": -24.476, "v3": 5.818, "v4": 18.922, "amplitude": 36.790, "phase_angle": 131.704, "puckering": "C1'-exo", "sugar_class": "~C2'-endo", "bin": "trig", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.011, "frame": { "rmsd": 0.011, "origin": [ 10.934, 15.146, 31.985 ], "x_axis": [ 0.825, -0.326, -0.461 ], "y_axis": [ -0.344, 0.358, -0.868 ], "z_axis": [ 0.449, 0.875, 0.183 ], "quaternion": [ 0.769, -0.566, 0.296, 0.006 ] } } ], "num_hbonds": 28, "hbonds": [ { "index": 1, "atom1_serNum": 12, "atom2_serNum": 413, "donAcc_type": "standard", "distance": 2.863, "atom1_id": "///A/1/O2", "atom2_id": "///B/20/N2", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 2, "atom1_serNum": 13, "atom2_serNum": 411, "donAcc_type": "standard", "distance": 2.889, "atom1_id": "///A/1/N3", "atom2_id": "///B/20/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 3, "atom1_serNum": 15, "atom2_serNum": 390, "donAcc_type": "standard", "distance": 3.476, "atom1_id": "///A/1/N4", "atom2_id": "///B/19/O4", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 4, "atom1_serNum": 15, "atom2_serNum": 410, "donAcc_type": "standard", "distance": 2.966, "atom1_id": "///A/1/N4", "atom2_id": "///B/20/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 5, "atom1_serNum": 35, "atom2_serNum": 390, "donAcc_type": "standard", "distance": 2.853, "atom1_id": "///A/2/N6", "atom2_id": "///B/19/O4", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 6, "atom1_serNum": 36, "atom2_serNum": 388, "donAcc_type": "standard", "distance": 2.910, "atom1_id": "///A/2/N1", "atom2_id": "///B/19/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 7, "atom1_serNum": 57, "atom2_serNum": 370, "donAcc_type": "standard", "distance": 3.009, "atom1_id": "///A/3/N6", "atom2_id": "///B/18/O4", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 8, "atom1_serNum": 58, "atom2_serNum": 368, "donAcc_type": "standard", "distance": 2.824, "atom1_id": "///A/3/N1", "atom2_id": "///B/18/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 9, "atom1_serNum": 79, "atom2_serNum": 350, "donAcc_type": "standard", "distance": 3.354, "atom1_id": "///A/4/N6", "atom2_id": "///B/17/O4", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 10, "atom1_serNum": 80, "atom2_serNum": 348, "donAcc_type": "standard", "distance": 2.751, "atom1_id": "///A/4/N1", "atom2_id": "///B/17/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 11, "atom1_serNum": 86, "atom2_serNum": 422, "donAcc_type": "acceptable", "distance": 3.061, "atom1_id": "///A/5/OP2", "atom2_id": "///A/25/O2", "atom_pair": "O:O", "residue_pair": "nt:ligand" }, { "index": 12, "atom1_serNum": 98, "atom2_serNum": 422, "donAcc_type": "acceptable", "distance": 2.892, "atom1_id": "///A/5/N7", "atom2_id": "///A/25/O2", "atom_pair": "N:O", "residue_pair": "nt:ligand" }, { "index": 13, "atom1_serNum": 101, "atom2_serNum": 331, "donAcc_type": "standard", "distance": 2.771, "atom1_id": "///A/5/O6", "atom2_id": "///B/16/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 14, "atom1_serNum": 102, "atom2_serNum": 329, "donAcc_type": "standard", "distance": 2.872, "atom1_id": "///A/5/N1", "atom2_id": "///B/16/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 15, "atom1_serNum": 104, "atom2_serNum": 328, "donAcc_type": "standard", "distance": 2.838, "atom1_id": "///A/5/N2", "atom2_id": "///B/16/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 16, "atom1_serNum": 121, "atom2_serNum": 426, "donAcc_type": "acceptable", "distance": 2.924, "atom1_id": "///A/6/N7", "atom2_id": "///A/25/O4", "atom_pair": "N:O", "residue_pair": "nt:ligand" }, { "index": 17, "atom1_serNum": 124, "atom2_serNum": 311, "donAcc_type": "standard", "distance": 2.807, "atom1_id": "///A/6/N6", "atom2_id": "///B/15/O4", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 18, "atom1_serNum": 124, "atom2_serNum": 426, "donAcc_type": "acceptable", "distance": 3.237, "atom1_id": "///A/6/N6", "atom2_id": "///A/25/O4", "atom_pair": "N:O", "residue_pair": "nt:ligand" }, { "index": 19, "atom1_serNum": 125, "atom2_serNum": 309, "donAcc_type": "standard", "distance": 2.837, "atom1_id": "///A/6/N1", "atom2_id": "///B/15/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 20, "atom1_serNum": 146, "atom2_serNum": 291, "donAcc_type": "standard", "distance": 2.982, "atom1_id": "///A/7/N6", "atom2_id": "///B/14/O4", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 21, "atom1_serNum": 147, "atom2_serNum": 289, "donAcc_type": "standard", "distance": 2.840, "atom1_id": "///A/7/N1", "atom2_id": "///B/14/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 22, "atom1_serNum": 168, "atom2_serNum": 271, "donAcc_type": "standard", "distance": 2.947, "atom1_id": "///A/8/N6", "atom2_id": "///B/13/O4", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 23, "atom1_serNum": 169, "atom2_serNum": 269, "donAcc_type": "standard", "distance": 2.777, "atom1_id": "///A/8/N1", "atom2_id": "///B/13/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 24, "atom1_serNum": 190, "atom2_serNum": 251, "donAcc_type": "standard", "distance": 2.922, "atom1_id": "///A/9/N6", "atom2_id": "///B/12/O4", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 25, "atom1_serNum": 191, "atom2_serNum": 249, "donAcc_type": "standard", "distance": 2.760, "atom1_id": "///A/9/N1", "atom2_id": "///B/12/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 26, "atom1_serNum": 212, "atom2_serNum": 232, "donAcc_type": "standard", "distance": 3.043, "atom1_id": "///A/10/O6", "atom2_id": "///B/11/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 27, "atom1_serNum": 213, "atom2_serNum": 230, "donAcc_type": "standard", "distance": 2.926, "atom1_id": "///A/10/N1", "atom2_id": "///B/11/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 28, "atom1_serNum": 215, "atom2_serNum": 229, "donAcc_type": "standard", "distance": 2.720, "atom1_id": "///A/10/N2", "atom2_id": "///B/11/O2", "atom_pair": "N:O", "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": "1g4q", "num_naChains": 2, "naChains": "A=10,B=10", "num_atoms": 562, "num_waters": 137, "num_metals": 3, "metals_desc": "Ca=3", "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": 8, "auxfiles": [ { "index": 1, "name": "dssr-pairs.pdb", "desc": "an ensemble of base pairs" }, { "index": 2, "name": "dssr-stems.pdb", "desc": "an ensemble of stems" }, { "index": 3, "name": "dssr-helices.pdb", "desc": "an ensemble of helices (coaxial stacking)" }, { "index": 4, "name": "dssr-2ndstrs.bpseq", "desc": "secondary structure in bpseq format" }, { "index": 5, "name": "dssr-2ndstrs.ct", "desc": "secondary structure in connectivity table format" }, { "index": 6, "name": "dssr-2ndstrs.dbn", "desc": "secondary structure in dot-bracket notation" }, { "index": 7, "name": "dssr-torsions.txt", "desc": "backbone torsion angles and suite names" }, { "index": 8, "name": "dssr-atom2bases.pdb", "desc": "an ensemble of atom-base stacking interactions" } ], "time_used": "999" } }