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![[Figure 1]](qe5008fig1mag.jpg)
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Figure 1
Protocol used to localize and analyze residues with questionable conformations in the PR2 structure model (PDB entry 1hsi). Step 1 corresponds to energy minimization of the X-ray model. Step 2 corresponds to simplification of the X-ray and minimized models into structural-letter sequences using HMM-SA (Camproux et al., 2004  ). Each structural letter represents the geometry of a four-Cα-atom fragment. Step 3 involves locating residues that have different structural letters in the sequences of X-ray and minimized models. These residues are highlighted in magenta in structural-letter sequences. In step 3, we compute the backbone-fragment r.m.s.d. (RMSDfrag) between X-ray and minimized models, considering four-Cα-atom fragments corresponding to residues with different letters in both models. Step 4: according to these results, residues with different structural letters between two models and RMSDfrag ≥ 0.10 Å are classified as RDC residues. These RDC residues are considered to be residues with questionable conformations. Other residues are classified as RCC and considered to have well supported conformations. RDC residues are highlighted in red in the structural-letter sequences of PDB entry 1hsi. In step 5, the number of RDC residues per X-ray model is normalized by the length of the protein to compute the proportion of residues with questionable conformations per X-ray model, denoted as PDC. In step 6, we explore the relationship between PDC and several X-ray model properties, including the year of deposition, the protein length, the number of chains, the resolution, the crystal system and the CATH class. We also examine the link between RDC residues and residue flexibility, accessibility and the composition of amino acids and the structural letters. In step 6, PR2 is displayed as a putty cartoon, where the putty radius is proportional to the flexibility of residues, quantified by the B-factor values extracted from the PDB file. In all panels, RDC residues are highlighted in red. |
![[Figure 1]](qe5008fig1.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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