5D99

3DW4 redetermined by direct methods starting from random phase angles

Summary for 5D99

• Entry DOI: 10.2210/pdb5d99/pdb
• Descriptor: RNA (27-MER) hairpin from sarcin-ricin domain of E. coli 23S rRNA, GLYCEROL (3 entities in total)
• Functional Keywords: ab initio direct methods structure determination, hairpin rna, rna
• Biological source: Enterobacteria phage L1
• Total number of polymer chains: 1
• Total formula weight: 8850.38

Authors

Mooers, B.H.M. (deposition date: 2015-08-18, release date: 2016-04-13, Last modification date: 2024-03-06)

Primary citation

Mooers, B.H.
Direct-methods structure determination of a trypanosome RNA-editing substrate fragment with translational pseudosymmetry.
Acta Crystallogr D Struct Biol, 72:477-487, 2016

PubMed Abstract: Using direct methods starting from random phases, the crystal structure of a 32-base-pair RNA (675 non-H RNA atoms in the asymmetric unit) was determined using only the native diffraction data (resolution limit 1.05 Å) and the computer program SIR2014. The almost three helical turns of the RNA in the asymmetric unit introduced partial or imperfect translational pseudosymmetry (TPS) that modulated the intensities when averaged by the l Miller indices but still escaped automated detection. Almost six times as many random phase sets had to be tested on average to reach a correct structure compared with a similar-sized RNA hairpin (27 nucleotides, 580 non-H RNA atoms) without TPS. More sensitive methods are needed for the automated detection of partial TPS.

PubMed: 27050127
DOI: 10.1107/S2059798316001224

Experimental method

X-RAY DIFFRACTION (0.97 Å)