Table 2. Statistics of x-ray diffraction... | Rockefeller University Press

Table 2.

Statistics of x-ray diffraction data and structure refinement

Parameters	Ligand
	0 mM GRGDSP (Mn/Ca), 4 h	10 mM GRGDSP (Mg/Ca), 24 h	1 mM GRGDSP (Mn/Ca), 4 h	3 mM GRGDSP (Mn/Ca), 4 h	5 mM GRGDSP (Mn/Ca), 4 h	10 mM GRGDSP (Mn/Ca), 4 h
Space group	P2₁2₁2	P2₁2₁2	P2₁2₁2	P2₁2₁2	P2₁2₁2	P2₁2₁2
Unit cell a, b, c (Å)	259.7, 145.0, 104.8	257.8, 145.3, 106.1	259.6, 144.5, 104.8	259.6, 144.7, 104.6	259.0, 144.6, 104.7	233.2, 143.6, 104.7
α, β, γ (°)	90, 90, 90	90, 90, 90	90, 90, 90	90, 90, 90	90, 90, 90	90, 90, 90
Wavelength (Å)	0.97934	0.97934	1.03320	1.03320	1.03320	0.97934
Resolution (Å)	50–2.45/2.58–2.45^a	50–2.45/2.51–2.45^a	50–2.75/2.82–2.75^a	50–2.95/3.03–2.95^a	50–3.00/3.08–3.00^a	50–2.35/2.41–2.35^a
Number of reflections (total/unique)	1,096,275/145,557	975,256/146,427	676,162/102,899	399,094/83,398	371,307/78,003	1,080,830/146,644
Completeness (%)	99.9/99.9^a	99.9/99.5^a	99.8/100.0^a	99.7/99.6^a	98.4/96.4^a	100.0/99.8^a
I/σ(I)	10.2/2.8^a	7.0/1.6^a	10.1/1.8^a	9.5/1.7^a	9.5/1.6^a	11.0/1.9^a
R_merge (%)^b	15.0/81.1^a	19.8/139.1^a	11.8/110.6^a	11.0/112.4^a	10.6/117.8^a	13.9/93.7^a
R_work/R_free^c	0.163/0.197	0.182/0.216	0.184/0.221	0.185/0.243	0.175/0.233	0.175/0.204
RMSD: bond (Å)	0.007	0.005	0.005	0.005	0.005	0.006
Angle (°)	0.658	0.570	0.591	0.566	0.560	0.676
Ramachandran plot (%)^d	96.4/3.3/0.3	96.2/3.6/0.2	95.9/3.6/0.5	95.6/4.1/0.3	95.1/4.6/0.3	94.5/5.3/0.2
Molecules/asymmetric unit	2	2	2	2	2	2
Residues, αIIb/β3	1–457 (453)/3–466 (471)^e	1–454 (453)/3–466 (471)^e	1–455 (453)/1–466 (471)^e	1–455 (453)/1 (3)–466 (471)^e	1–455 (453)/3–466 (471)^e	1–454 (453)/3 (59)–471 (433)^e
Numbers of amino acid/carbohydrate/water	2,703/15/1,324	2,711/14/887	2,712/15/540	2,714/14/327	2,713/14/303	2,615/13/1,318
Conformational states (molecule 1/molecule 2)^f	State 1/State 1	State 2/State 1	State 7/State 3	State 7/State 4	State 7/State 5	State 6/State 8
PDB accession no.	3ZDX	3ZDY	3ZDZ	3ZE0	3ZE1	3ZE2

Parameters	Ligand
	0 mM GRGDSP (Mn/Ca), 4 h	10 mM GRGDSP (Mg/Ca), 24 h	1 mM GRGDSP (Mn/Ca), 4 h	3 mM GRGDSP (Mn/Ca), 4 h	5 mM GRGDSP (Mn/Ca), 4 h	10 mM GRGDSP (Mn/Ca), 4 h
Space group	P2₁2₁2	P2₁2₁2	P2₁2₁2	P2₁2₁2	P2₁2₁2	P2₁2₁2
Unit cell a, b, c (Å)	259.7, 145.0, 104.8	257.8, 145.3, 106.1	259.6, 144.5, 104.8	259.6, 144.7, 104.6	259.0, 144.6, 104.7	233.2, 143.6, 104.7
α, β, γ (°)	90, 90, 90	90, 90, 90	90, 90, 90	90, 90, 90	90, 90, 90	90, 90, 90
Wavelength (Å)	0.97934	0.97934	1.03320	1.03320	1.03320	0.97934
Resolution (Å)	50–2.45/2.58–2.45^a	50–2.45/2.51–2.45^a	50–2.75/2.82–2.75^a	50–2.95/3.03–2.95^a	50–3.00/3.08–3.00^a	50–2.35/2.41–2.35^a
Number of reflections (total/unique)	1,096,275/145,557	975,256/146,427	676,162/102,899	399,094/83,398	371,307/78,003	1,080,830/146,644
Completeness (%)	99.9/99.9^a	99.9/99.5^a	99.8/100.0^a	99.7/99.6^a	98.4/96.4^a	100.0/99.8^a
I/σ(I)	10.2/2.8^a	7.0/1.6^a	10.1/1.8^a	9.5/1.7^a	9.5/1.6^a	11.0/1.9^a
R_merge (%)^b	15.0/81.1^a	19.8/139.1^a	11.8/110.6^a	11.0/112.4^a	10.6/117.8^a	13.9/93.7^a
R_work/R_free^c	0.163/0.197	0.182/0.216	0.184/0.221	0.185/0.243	0.175/0.233	0.175/0.204
RMSD: bond (Å)	0.007	0.005	0.005	0.005	0.005	0.006
Angle (°)	0.658	0.570	0.591	0.566	0.560	0.676
Ramachandran plot (%)^d	96.4/3.3/0.3	96.2/3.6/0.2	95.9/3.6/0.5	95.6/4.1/0.3	95.1/4.6/0.3	94.5/5.3/0.2
Molecules/asymmetric unit	2	2	2	2	2	2
Residues, αIIb/β3	1–457 (453)/3–466 (471)^e	1–454 (453)/3–466 (471)^e	1–455 (453)/1–466 (471)^e	1–455 (453)/1 (3)–466 (471)^e	1–455 (453)/3–466 (471)^e	1–454 (453)/3 (59)–471 (433)^e
Numbers of amino acid/carbohydrate/water	2,703/15/1,324	2,711/14/887	2,712/15/540	2,714/14/327	2,713/14/303	2,615/13/1,318
Conformational states (molecule 1/molecule 2)^f	State 1/State 1	State 2/State 1	State 7/State 3	State 7/State 4	State 7/State 5	State 6/State 8
PDB accession no.	3ZDX	3ZDY	3ZDZ	3ZE0	3ZE1	3ZE2

Mg/Ca, 5 mM Mg²⁺/1 mM Ca²⁺; Mn/Ca, 2 mM Mn²⁺/0.1 mM Ca²⁺; RMSD, Root-mean-square deviation; PDB, Protein Data Bank.

Numbers correspond to the last resolution shell.

R_merge = ∑_h∑_i|I_i(h) − < I(h) > |/∑_h∑_i|I_i(h)|, in which I_i(h) and < I(h) > are the ith and mean measurement of the intensity of reflection h.

R_work = ∑_h||F_obs (h)| − |F_calc (h)||/∑_h|F_obs (h)|, in which F_obs (h) and F_calc (h) are the observed and calculated structure factor amplitudes, respectively. No I/σ(I) cutoff was applied. R_free is the R value obtained for a test set of reflections consisting of a randomly selected 0.6% subset of data excluded from refinement.

Residues in favorable, allowed, and outlier regions of the Ramachandran plot are as reported by MolProbity.

Numbers in parenthesis correspond to chains C and D.

Molecule 1 = chains A and B; and molecule 2 = chains C and D.

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