Page 46 - The autoimmune hypothesis of narcolepsy and its unexplored clinical features M.S. Schinkelshoek
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Chapter 3
collected at the mx2 beamline of the Australian Synchrotron using a ADSC Q315r detector and data processing was carried out with XDS (Kabsch, 2010) and Scala (Evans, 2006). The crystal structures were solved by molecular replacement in Phaser (McCoy et al., 2007) using a published HLA-DQ6 structure (PDB code 1UVQ) as search model. The structural models were refined by iterative rounds of model building in Coot (Emsley et al., 2010) and restrained refinement in Phenix (Adams et al., 2010). For further details on data collection and refinement statistics, see Table 3.1.
Table 3.1. Data collection and refinement statistics. HA = hemagglutinin; Hcrt = hypocretin
 Wavelength
Resolution range
Space group Unit cell
Total reflections Unique reflections Multiplicity Completeness (%) Mean I/sigma(I) Wilson B-factor R-merge
CC1/2
CC*
R-work
R-free
Number of non-hydrogen atoms
Macromolecules Ligands
Solvent
Protein residues
RMS (bonds)
RMS (angles) Ramachandran favored (%) Ramachandran allowed (%) Ramachandran outliers (%) Rotamer outliers (%) Clashscore
Average B-factor Macromolecules Ligands
Solvent
HLA-DQ6- Hcrt56-68
34.52 - 2.0 (2.071 - 2.0)
C 1 2 1
163.063 72.404 99.277
90 113.763 90
137291 (13803) 70012 (6989) 2.0 (2.0) 97.65 (97.90) 7.34 (1.86) 22.44 0.06104 (0.3654) 0.995 (0.835) 0.999 (0.954) 0.1755 (0.2524) 0.1980 (0.2795) 6888
6044
76
768
751
0.008
1.17
98.09
1.91
0.00
0.60
5.44
43.49 43.27 69.59 42.63
HLA-DQ6- Hcrt87-99
39.56 - 1.936 (2.005 - 1.936)
P 2 21 21
72.538 99.549 148.372 90 90 90
160661 (15461) 80479 (7782) 2.0 (2.0) 99.54 (97.12) 9.85 (2.37) 23.29 0.03506 (0.2447) 0.999 (0.948) 1 (0.987) 0.1882 (0.2668) 0.2157 (0.2819) 6696
5990
90
616
745
0.009
1.25
97.65
2.35
0.00
1.21
5.58
45.13 44.94 77.29 42.29
HLA-DQ6-H1N1- HA275-287
40.11 - 1.7 (1.761 - 1.7)
P 21 21 21
55.764 89.58 115.484 90 90 90
126644 (12583) 64298 (6352) 2.0 (2.0) 99.84 (99.95) 10.47 (2.31) 17.15 0.04976 (0.3822) 0.994 (0.685) 0.999 (0.902) 0.1705 (0.2377) 0.1972 (0.2680) 3720
3083
95
542
384
0.009
1.46
97.61
2.39
0.00
0.59
4.36
26.10 22.61 77.67 36.94
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