Crystal structure of Saccharomyces cerevisiae 6-phosphogluconate dehydrogenase Gnd1

BMC Structural Biology

Table 1 Data Collection and Refinement Statistics.

Data collection
Space group	P 6₅22
Unit-cell parameters (Å)	a = b = 147.26, c = 114.42,α=β = 90°, γ = 120°
Wavelength (Å)	1.5418
Total reflections	347,811
Unique reflections	29,518
Completeness (%), overall/outer shell	96.9% (94.0%)
Resolution range (Å), overall/outer shell	21.32–2.37 (2.45–2.37)
Refinement statistics
Rmerge^a (%) overall/outer shell	7.41 (36.29)
R-factor^b (%)	20.8
R-free^c (%)	21.8
Number of atoms
Protein	3,683
Water	212
Citrate molecule	32
Rms deviation from target^d
Bond lengths (Å)	0.009
Bond angles (°)	1.3
Average B factors:
Protein atoms	49.1
Water atoms	52.8
Citrate atoms	61.7
Ramachandran plot (%)^e	91.7/7.6/0.7/0

^a $R_{m e r g e} = \frac{\sum_{h} \sum_{i} | I_{h i} - 〈 I_{h} 〉 |}{\sum_{h} \sum_{i} I_{h i}}$ , where I_hi is the i^th observation of the reflection h, while I_h is the mean intensity of reflection h.
^b $R_{f a c t o r} = \sum \frac{| | F_{o b s} | - | F_{c a l c} | |}{| F_{o b s} |}$ , where F_obsand F_calcare the observed and calculated structure factor amplitudes, respectively.
^c R_free was calculated with a small fraction (5%) of randomly selected reflections. No refinement was done on the 5% of randomly selected reflections at any stage.
^d Root-mean-square deviation of bond lengths or bond angles from ideal geometry.
^e Percentage of residues in most favoured/additionally allowed/generously allowed/disallowed regions of Ramachandran plot, according to PROCHECK.

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