Table II. Rerefined α IIb β 3 complex... | Rockefeller University Press

Table II.

Rerefined α_IIbβ₃ complex x-ray diffraction and refinement data

Ligand	Native1	Native2	Tirofiban	Eptifibatide	L-739758
Space group	P3₂21	P3₂21	P3₂21	P3₂21	P3₂21
Unit cell (a, b, c) (Å)	148.9, 148.9, 176.1	148.9, 148.9, 176.4	148.6, 148.6, 177.2	149.6, 149.6, 175.7	149.2, 149.2, 176.2
α, β, γ (degree)	90, 90, 120	90, 90,120	90, 90, 120	90, 90, 120	90, 90, 120
Wavelength (Å)	0.9793	0.9793	0.9760	0.9760	0.9793
Resolution (Å)	50–2.8	50–2.75	50–2.9	50–2.9	50–3.1
Number of reflections (total/unique)	400,460/55,875	442,121/62,512	330,745/50,662	357,439/50,647	263,308/41,586
Completeness (%)	99.9/99.8^{^b}	99.9/100^{^b}	99.7/98.2^{^b}	100/100^{^b}	99.8/99.7^{^b}
I/σ (I)	14.0/3.1^{^b}	20.0/3.0^{^b}	12.1/2.0^{^b}	14.9/2.7^{^b}	12.1/2.7^{^b}
R_merge (%)	13.0/68.1^{^b}	9.6/59.8^{^b}	13.9/57.8^{^b}	11.7/61.5^{^b}	14.0/55.8^{^b}
Number of atoms (protein/water/other)	10,404/612/210	10,461/1,129/210	10,363/355/235	10,385/364/223	10,348/98/240
R_msd bond lengths (Å)	0.005	0.006	0.005	0.005	0.007
R_msd bond angles (degree)	0.9	1.0	0.9	0.9	1.0
R_work (%)	16.1	14.4	16.7	16.3	18.1
R_free (%)	20.4	19.1	20.6	21.3	22.0
Ramachandran statistics (% favored/allowed/outlier)^{^a}	97.3/2.5/0.2	97.2/2.5/0.3	96.5/3.3/0.2	96.8/2.9/0.2	96.5/3.3/0.2
Obsolete PDB code	1TY3	1TXV	1TY5	1TY6	1TY7
New PDB code	2VDK	2VDL	2VDM	2VDN	2VC2

Ligand	Native1	Native2	Tirofiban	Eptifibatide	L-739758
Space group	P3₂21	P3₂21	P3₂21	P3₂21	P3₂21
Unit cell (a, b, c) (Å)	148.9, 148.9, 176.1	148.9, 148.9, 176.4	148.6, 148.6, 177.2	149.6, 149.6, 175.7	149.2, 149.2, 176.2
α, β, γ (degree)	90, 90, 120	90, 90,120	90, 90, 120	90, 90, 120	90, 90, 120
Wavelength (Å)	0.9793	0.9793	0.9760	0.9760	0.9793
Resolution (Å)	50–2.8	50–2.75	50–2.9	50–2.9	50–3.1
Number of reflections (total/unique)	400,460/55,875	442,121/62,512	330,745/50,662	357,439/50,647	263,308/41,586
Completeness (%)	99.9/99.8^b	99.9/100^b	99.7/98.2^b	100/100^b	99.8/99.7^b
I/σ (I)	14.0/3.1^b	20.0/3.0^b	12.1/2.0^b	14.9/2.7^b	12.1/2.7^b
R_merge (%)	13.0/68.1^b	9.6/59.8^b	13.9/57.8^b	11.7/61.5^b	14.0/55.8^b
Number of atoms (protein/water/other)	10,404/612/210	10,461/1,129/210	10,363/355/235	10,385/364/223	10,348/98/240
R_msd bond lengths (Å)	0.005	0.006	0.005	0.005	0.007
R_msd bond angles (degree)	0.9	1.0	0.9	0.9	1.0
R_work (%)	16.1	14.4	16.7	16.3	18.1
R_free (%)	20.4	19.1	20.6	21.3	22.0
Ramachandran statistics (% favored/allowed/outlier)^a	97.3/2.5/0.2	97.2/2.5/0.3	96.5/3.3/0.2	96.8/2.9/0.2	96.5/3.3/0.2
Obsolete PDB code	1TY3	1TXV	1TY5	1TY6	1TY7
New PDB code	2VDK	2VDL	2VDM	2VDN	2VC2

R_merge = Σ_H Σ_i |I_i(h) − <I(h)>|/Σ_HΣ_i I_i(h), where I_i(h) and <I(h)> are the ith and mean measurement of the intensity of reflection, h. R_work = Σ_H||F_obs (h)| − |F_calc (h)||/Σ_H|F_obs (h)|, where F_obs (h) and F_calc (h) are the observed and calculated structure factors, respectively. No I/σ cutoff was applied. R_free is the R value obtained for a test set of reflections consisting of a randomly selected 5% subset of the data set excluded from refinement.

Determined with RAMPAGE (Lovell et al., 2003).

These numbers correspond to the last resolution shell.

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