Correction: Consistent global structures of complex RNA states through multidimensional chemical mapping

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Cheng CY, Chou FC, Kladwang W, Tian S, Cordero P, Das R. 2015. Consistent global structures of complex RNA states through multidimensional chemical mapping. eLife 4:e07600. doi: 10.7554/eLife.07600

Published 2 June 2015

Table 1 has been corrected. The original manuscript used a previously published formula from Hajdin et al. RNA (2010) for estimating the p-value of a 3D RNA structure prediction but calculated these p-values using the incorrect mean RMSD values. When the correct parameters are used, the p-values of our predictions decrease, i.e. the estimated significances are increased. The conclusions of the manuscript are unchanged.

The corrected table is shown here, with changes highlighted:

Table 1 Corrected. Benchmark of multidimensional chemical mapping on RNAs with crystal structures

RNA	Length	M²/Rosetta (no MOHCA, control)		MCM
RNA	Length	RMSD to crystal (Å) (accuracy)	p-value§	RMSD to crystal (Å) (accuracy)	p-value§
Tetrahymena ribozyme P4–P6 domain	158	38.3	>0.9	8.6	<1.0 × 10⁻¹⁶
V. cholerae cyclic-di-GMP riboswitch aptamer, ligand-bound*	89	11.3	2.6 × 10⁻³	7.6	6.3 × 10⁻⁷
F. nucleatum double glycine riboswitch ligand-binding domain, ligand-bound*	159	30.5	>0.9	7.9	<1.0 × 10⁻¹⁶
S. thermophilum adenosylcobalamin riboswitch aptamer, ligand-bound*	168	17.1†	5.3 × 10⁻⁷	11.9	4.0 × 10⁻¹⁵
Class I ligase	127	26.3	>0.9	14.5	6.8 × 10⁻⁵
Class I ligase, core domain‡	87	14.0	0.13	11.1	3.1 × 10⁻³
D. iridis lariat-capping ribozyme	188	9.6†	<1.0 × 10⁻¹⁶	8.2	<1.0 × 10⁻¹⁶
D. iridis lariat-capping ribozyme, MCM refined regions‡	69	17.0†	n.a.§	11.2	n.a.§

* MCM modeling was performed with MOHCA-seq constraints from datasets collected on the ligand-bound state; ligands were not included during Rosetta modeling.

† M²/Rosetta statistics are reported for RNA-puzzle submission rank 1 models, which included subdomains built by homology modeling.

‡ Calculated over core domain residues or refined regions after alignment using MAMMOTH (Ortiz et al., 2002); see ‘Materials and methods’.

§ p-value computed using analytical formula for secondary-structure-constrained 3D modeling in (Hajdin et al., 2010); it is not applicable to peripheral domains. Value above 0.9 are not well-determined and are presented as > 0.9.

The originally published table is also shown for reference:

Table 1 Original. Benchmark of multidimensional chemical mapping on RNAs with crystal structures

RNA	Length	M²/Rosetta		MCM
RNA	Length	RMSD to crystal (Å) (accuracy)	p-value§	RMSD to crystal (Å) (accuracy)	p-value§
Tetrahymena ribozyme P4–P6 domain	158	38.3	1.0	8.6	5.1 × 10⁻¹²
V. cholerae cyclic-di-GMP riboswitch aptamer, ligand-bound*	89	11.3	0.28	7.6	4.3 × 10⁻³
F. nucleatum double glycine riboswitch ligand-binding domain, ligand-bound*	159	30.5	1.0	7.9	2.1 × 10⁻¹³
S. thermophilum adenosylcobalamin riboswitch aptamer, ligand-bound*	168	17.1†	3.9 × 10⁻³	11.9	1.5 × 10⁻⁸
Class I ligase	127	26.3	1.0	14.5	5.6 × 10⁻²
Class I ligase, core domain‡	87	14.0	0.86	11.1	0.30
D. iridis lariat-capping ribozyme	188	9.6†	1.2 × 10⁻¹⁵	8.2	<1.0 × 10⁻¹⁶
D. iridis lariat-capping ribozyme, MCM refined regions‡	69	17.0†	n.a.§	11.2	n.a.§

* MCM modeling was performed with MOHCA-seq constraints from datasets collected on the ligand-bound state; ligands were not included during Rosetta modeling.

† M²/Rosetta statistics are reported for RNA-puzzle submission rank 1 models, which included subdomains built by homology modeling.

‡ Calculated over core domain residues or refined regions after alignment using MAMMOTH (Ortiz et al., 2002); see ‘Materials and methods’.

§ p-value computed using analytical formula for secondary-structure-constrained 3D modeling in (Hajdin et al., 2010); it is not applicable to peripheral domains.

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Clarence Yu Cheng

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Fang-Chieh Chou

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Wipapat Kladwang

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Siqi Tian

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Pablo Cordero

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Rhiju Das

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Version of Record published: July 21, 2015

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