Insights into the Structures of DNA Damaged by Hydroxyl Radical: Crystal Structures of DNA Duplexes Containing 5-Formyluracil

Table 2

Crystal data and statistical information on data collection and processing and on structure determination.

Crystals	fUA^1	fUA^2	fUA^3	fUA^4	fUG^1	fUG^2	fUG^3
Wavelength (Å)	1.00	0.90	1.00	1.00	1.00	1.00	1.00
Beamline (at PF)	BL-18B	BL-6B	BL-18B	BL-6B	BL-18B	BL-18B	BL-18B
Oscillation ranges(∘)	5	3	5	5	3	2	2
Frames	72	60	34	36	60	90×2^c	90
Space group	P212121	P212121	P212121	P212121	P212121	P212121	P212121
a (Å)	25.8	26.0	25.2	25.3	24.6	25.3	25.0
b (Å)	39.3	39.5	41.2	41.7	40.0	40.3	40.5
c (Å)	65.0	65.7	65.4	66.0	68.5	66.0	66.8
Z ^a	1	1	1	1	1	1	1
Matthews coefficient (Å^3 Da^-1)	2.15	2.20	2.22	2.28	2.28	2.28	2.29
Solvent content (%)	42.9	44.2	44.6	45.9	46.0	46.1	46.3
Resolution (Å)	1.57	1.5	1.7	1.8	3.0	1.95	2.6
Completeness (%)	97.1	99.4	97.7	99.3	99.3	99.9	99.9
𝑅^bmerge (%)	3.1	4.8	2.9	2.8	11.4	4.0	6.3
Observed reflections	87588	66227	31872	45728	16654	72307	38399
Unique reflections	9502	10301	7779	6881	1531	5312	2342
Redundancy	9.22	6.43	4.10	6.65	10.9	13.6	16.4
Structure refinement ^f
Resolution range (Å)	10.0–1.57	10.0–1.55	10.0–1.85	10.0–1.80	15.0–3.02	10.0–1.95	10.0–2.70
R-factor (%)^d	18.3	18.3	21.6	19.3	18.8	20.3	21.1
𝑅free (%)^e	23.2	22.5	26.0	23.1	22.9	26.1	27.8
R.m.s. deviation
Bond distances (Å)	0.027	0.028	0.019	0.021	0.005	0.019	0.007
Bond angles (∘)	3.8	3.6	3.2	3.4	0.9	3.1	1.0
No. of ions	1Mg^2+, 1K^+	1Mg^2+	—	—	—	1Mg^2+	1Mg^2+
No. of additive molecules	—	—	—	—	—	1Hoechst33258	1DAPI
No. of water molecules	150	185	82	142	27	123	45
PDB-ID	1G75	1G8N	1G8U	1G8V	3AJJ	3AJK	3AJL

^aNumber of duplexes in the asymmetric unit. ^b𝑅_merge=100×∑_𝐡𝑗|𝐼_𝐡𝑗−⟨𝐼_𝐡⟩|/∑_𝐡𝑗𝐼_𝐡𝑗, where 𝐼_𝐡𝑗 is the 𝑗th measurement of the intensity of reflection h and ⟨𝐼_𝐡⟩ is its mean value. ^cTwo data sets were taken for a crystal by changing exposure time to compensate overloaded reflections. ^d𝑅-factor = 100 × ∑||𝐹_𝑜|−|𝐹_𝑐||/∑|𝐹_𝑜|, where |𝐹_𝑜| and |𝐹_𝑐| are the observed and calculated structure factor amplitudes, respectively. ^eCalculated using a random set containing 10% of observations that were not included throughout refinement [17].