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47.445, "v2": -41.373, "v3": 22.717, "v4": 6.991, "amplitude": 46.602, "phase_angle": 152.598, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "32p", "cluster": "1b", "suiteness": 0.120, "filter_rmsd": 0.062, "frame": { "rmsd": 0.010, "origin": [ -11.193, -23.702, 38.595 ], "x_axis": [ -0.847, -0.515, 0.128 ], "y_axis": [ -0.531, 0.828, -0.180 ], "z_axis": [ -0.014, -0.220, -0.975 ], "quaternion": [ -0.037, -0.274, 0.955, -0.105 ] } }, { "index": 14, "index_chain": 14, "chain_name": "A", "nt_resnum": 14, "nt_name": "DA", "nt_code": "A", "nt_id": "///A/14", "linked_nts": [ "///A/13", "///A/15" ], "nt_type": "DNA", "dbn": ".", "summary": "anti,~C2'-endo,BI,non-pair-contact,ss-non-loop", "alpha": -69.441, "beta": 151.610, "gamma": 39.768, "delta": 145.097, "epsilon": -174.456, "zeta": -84.592, "epsilon_zeta": -89.864, "bb_type": "BI", "chi": -95.989, "glyco_bond": "anti", "C5prime_xyz": [ -1.588, 7.860, -2.331 ], "P_xyz": [ 0.921, 8.282, -1.764 ], "form": "B", "ssZp": 1.014, "Dp": 1.704, "splay_angle": 18.988, "splay_distance": 3.348, "splay_ratio": 0.167, "d22": null, "d64": null, "eta": 170.797, "theta": -106.989, "eta_prime": -162.923, "theta_prime": -135.466, "eta_base": -109.124, "theta_base": -100.121, "v0": -14.918, "v1": 30.753, "v2": -35.044, "v3": 26.821, "v4": -7.754, "amplitude": 35.229, "phase_angle": 174.126, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "4b", "suiteness": 0.640, "filter_rmsd": 0.042, "frame": { "rmsd": 0.015, "origin": [ -11.019, -22.958, 34.823 ], "x_axis": [ -0.973, 0.212, -0.092 ], "y_axis": [ 0.224, 0.964, -0.146 ], "z_axis": [ 0.057, -0.162, -0.985 ], "quaternion": [ 0.038, 0.110, 0.990, -0.078 ] } }, { "index": 15, "index_chain": 15, "chain_name": "A", "nt_resnum": 15, "nt_name": "DG", "nt_code": "G", "nt_id": "///A/15", "linked_nts": [ "///A/14", "///A/16" ], "nt_type": "DNA", "dbn": ".", "summary": "anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate", "alpha": -71.299, "beta": 175.390, "gamma": 45.695, "delta": 121.680, "epsilon": -172.753, "zeta": -76.564, "epsilon_zeta": -96.189, "bb_type": "BI", "chi": -98.192, "glyco_bond": "anti", "C5prime_xyz": [ -3.421, 7.908, -2.248 ], "P_xyz": [ -1.708, 9.694, -2.995 ], "form": "B", "ssZp": 2.363, "Dp": 2.444, "splay_angle": 19.603, "splay_distance": 3.473, "splay_ratio": 0.174, "d22": null, "d64": null, "eta": 155.593, "theta": -154.486, "eta_prime": -175.949, "theta_prime": -172.360, "eta_base": -134.030, "theta_base": -120.947, "v0": -41.157, "v1": 41.837, "v2": -26.345, "v3": 3.536, "v4": 23.243, "amplitude": 42.516, "phase_angle": 128.290, "puckering": "C1'-exo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.009, "frame": { "rmsd": 0.009, "origin": [ -11.640, -23.137, 31.538 ], "x_axis": [ -0.761, 0.646, -0.056 ], "y_axis": [ 0.646, 0.748, -0.148 ], "z_axis": [ -0.054, -0.149, -0.987 ], "quaternion": [ 0.000, 0.346, 0.935, -0.080 ] } }, { "index": 16, "index_chain": 16, "chain_name": "A", "nt_resnum": 16, "nt_name": "DC", "nt_code": "C", "nt_id": "///A/16", "linked_nts": [ "///A/15", null ], "nt_type": "DNA", "dbn": ".", "summary": "anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate", "alpha": -108.395, "beta": 89.387, "gamma": 165.107, "delta": 147.941, "epsilon": null, "zeta": null, "epsilon_zeta": null, "bb_type": "--", "chi": -148.878, "glyco_bond": "anti", "C5prime_xyz": [ -1.786, 8.731, 0.481 ], "P_xyz": [ -0.849, 10.208, -1.455 ], "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": -19.757, "v1": 38.105, "v2": -40.844, "v3": 29.860, "v4": -6.735, "amplitude": 41.424, "phase_angle": 170.398, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22t", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.061, "frame": { "rmsd": 0.009, "origin": [ -13.073, -22.563, 28.427 ], "x_axis": [ -0.251, 0.960, -0.121 ], "y_axis": [ 0.960, 0.231, -0.161 ], "z_axis": [ -0.127, -0.156, -0.980 ], "quaternion": [ -0.002, 0.612, 0.785, -0.101 ] } } ], "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": "8v5j", "num_naChains": 1, "naChains": "A=16", "num_atoms": 620, "num_waters": 104, "num_metals": 9, "metals_desc": "Ca=9", "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": 9, "auxfiles": [ { "index": 1, "name": "dssr-2ndstrs.bpseq", "desc": "secondary structure in bpseq format" }, { "index": 2, "name": "dssr-2ndstrs.ct", "desc": "secondary structure in connectivity table format" }, { "index": 3, "name": "dssr-2ndstrs.dbn", "desc": "secondary structure in dot-bracket notation" }, { "index": 4, "name": "dssr-torsions.txt", "desc": "backbone torsion angles and suite names" }, { "index": 5, "name": "dssr-stacks.pdb", "desc": "an ensemble of base stacks" }, { "index": 6, "name": "dssr-rotmat.txt", "desc": "position vector and rotation matrix" }, { "index": 7, "name": "dssr-viewV.pdb", "desc": "vertical view of the principal moment of inertia" }, { "index": 8, "name": "dssr-viewH.pdb", "desc": "horizontal view of the principal moment of inertia" }, { "index": 9, "name": "dssr-viewT.pdb", "desc": "top view of the principal moment of inertia" } ], "time_used": "999" } }