. Author manuscript; available in PMC: 2019 Jul 3.

Published in final edited form as: Biochemistry. 2018 May 18;57(26):3916–3924. doi: 10.1021/acs.biochem.8b00367

Table 1.

Data collection and refinement statistics for HDAC6-inhibitor complexes

Inhibitor	1	2	3	4
Unit Cell
Space group	P2₁2₁2₁	P2₁2₁2₁	P2₁2₁2₁	P2₁2₁2₁
a, b, c (Å)	74.8, 91.9, 96.4	74.7, 91.8, 96.5	74.7, 91.8, 96.5	74.8, 92.0, 96.6
α, β, γ (°)	90, 90, 90	90, 90, 90	90, 90, 90	90, 90, 90
Data Collection
Wavelength (Å)	0.97946	0.97946	0.97946	0.97933
Resolution (Å)	48.2 – 1.62	59.08 – 1.24	96.60 – 2.03	96.64 – 1.70
Total/unique no. of reflections	528011 / 84908	1156727 / 188513	271026 / 43532	507763 / 74006
R_merge^a,^b	0.189 (0.816)	0.101 (0.593)	0.228 (0.538)	0.224 (1.558)
R_p.i.m.^a,^c	0.082 (0.346)	0.044 (0.257)	0.099 (0.229)	0.91 (0.670)
CC_1/2^a,^d	0.969 (0.682)	0.997 (0.871)	0.988 (0.850)	0.991 (0.605)
I/σ(I)^a	6.7 (2.2)	10.0 (3.0)	6.3 (3.6)	8.6 (3.4)
Redundancy^a	6.2	6.1 (6.2)	6.2 (6.4)	6.9 (6.3)
Completeness (%)^a	99.5 (99.7)	99.7 (99.9)	99.8 (100)	100 (100)
Refinement
No. of reflections used in refinement/test set	84783 (8378)	188358 (18683)	43445 (4284)	73824 (7278)
R_work^a,^e	0.170 (0.262)	0.127 (0.177)	0.176 (0.221)	0.169 (0.220)
R_free^a,^e	0.219 (0.338)	0.153 (0.219)	0.223 (0.266)	0.194 (0.256)
No. of nonhydrogen atoms:
protein	5721	5838	5563	5689
ligand	74	125	26	60
solvent	764	935	648	654

Average B-factors (Å²)

protein	11	10	10	10
ligand	17	20	7	19
solvent	23	24	17	23

Root-mean-square deviation from ideal geometry

bonds (Å)	0.006	0.008	0.003	0.003
angles (°)	0.8	1.0	0.6	0.7
Ramachandran plot (%)^f
favored	97.75	97.61	97.60	97.61
allowed	2.25	2.39	2.40	2.39

PDB accession code	6CSR	6CSP	6CSQ	6CSS

Values in parentheses refer to the data from the highest resolution shell.

R_merge = Σ_hklΣ_i|I_i,hkl − 〈I〉 _hkl|/Σ_hklΣ_i I_i,hkl, where 〈I〉_hkl is the average intensity calculated for reflection hkl from replicate measurements.

R_p.i.m.= (Σ_hkl(1/(N-1))^1/2 Σ_i|I_i,hkl − 〈I〉_hkl|)/Σ_hklΣ_i I_i,hkl, where 〈I〉_hkl is the average intensity calculated for reflection hkl from replicate measurements and N is the number of reflections

Pearson correlation coefficient between random half-datasets.

R_work = Σ||F_o| − |F_c||/Σ|F_o| for reflections contained in the working set. |F_o| and |F_c| are the observed and calculated structure factor amplitudes, respectively. R_free is calculated using the same expression for reflections contained in the test set held aside during refinement.

Calculated with PROCHECK.