Structural and Functional Analysis of the Complex between Citrate and the Zinc Peptidase Carboxypeptidase A

Table 1

Statistics of data collection and refinement for citrate-bound CPA.

Parameters	Value
Wavelength used during data collection	0.8123 Å
Unit cell constants	𝑎=40.61Å, 𝑏=57.01Å, 𝑐=60.61Å 𝛼= 90.0°,𝛽= 102.4°,𝛾= 90.0°
Resolution range	20.24–1.70 Å
Space group	P21 (1 mol/asymmetric unit)
Number of measured reflections	185,198
Number of unique reflections	29,594
𝑅^amerge (overall/outermost shell)	7.8/27.9%
Completeness & multiplicity (overall/outermost shell)	99.6/99.8%; 2.9/3.1
I/σI (overall/outermost shell)	18.1/3.5
Reflections used for refinement (total/test set)	26,403/893
Crystallographic 𝑅^bfactor/𝑅^cfree	17.8/20.5%
Deviation from ideality
r.m.s.d. bond lengths	0.009 Å
r.m.s.d. bond angles	1.18°
Number of protein atoms/total atoms	2,415/2,691
B-factor statistics (Å^2)
Overall B-factor/Wilson plot B-factor	17.6/25.4
Catalytic domain, main/side chain	16.2/17.0
Zn^2+ (1 in total/1 mol per monomer)	13.6
Citrate atoms (13 in total/1 mol per monomer)	20.6
Glycerol atoms (36 in total/6 mols per monomer)	35.4
Solvent atoms (214 in total)	26.3
Protein geometry ^d
Ramachandran favored	96.7% (294 of 304 residues)
Ramachandran allowed	99.7% (303 of 304 residues)
Ramachandran outliers	0.3% (1 of 304 residues, Ser-199)
Residues with bad bonds/angles	0.00/0.00%
Rotamer outliers	0.33%

Notes: ^a𝑅_merge=Σ_hklΣ_𝑗=1to𝑁|𝐼_hkl−𝐼_hkl,(𝑗)|/Σ_hklΣ_𝑗=1to𝑁_Ihkl(𝑗), where N is the redundancy of the data. The outermost shell is 1.75–1.70 Å.
^b𝑅_factor=Σ_hkl||𝐹_obs|−|𝐹_calc||/Σ_hkl|𝐹_obs|, where the 𝐹_obs and 𝐹_calc are the observed and calculated structure factor amplitudes of reflection hkl.
^c𝑅_free = is equal to 𝑅_factor for a randomly selected 3.3% subset of reflections that were not used in refinement.
^dAccording to Molprobity [37].