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. Author manuscript; available in PMC: 2020 Dec 10.
Published in final edited form as: Biochemistry. 2019 Dec 2;58(49):4912–4924. doi: 10.1021/acs.biochem.9b00934

Table 1.

Data Collection and Refinement Statistics for HDAC6 CD1–Inhibitor Complexesa

Data collection HDAC6 CD1–
Trichostatin A		 HDAC6 CD1–
AR–42		 Y363F HDAC6
CD1–
Trichostatin A		 Y363F HDAC6
CD1–AR-42		 K330L HDAC6
CD1–AR-42		 K330L HDAC6
CD1–
Resminostat		 K330L HDAC6
CD1–Givinostat
Space group P 21 P 21 21 21 P 21 P 21 21 21 P 21 21 21 P 21 21 21 P 21 21 21
a,b,c (Å) 53.0 124.2 55.5 54.7 61.0 121.6 52.8 124.4 55.6 54.5 60.5 121.9 55.0 60.6 121.8 67.2 102.6 112.9 55.1 60.4 122.1
α,β,γ (°) 90.0 114.0 90.0 90.0 90.0 90.0 90.0 114.4 90.0 90.0 90.0 90.0 90.0 90.0 90.0 90.0 90.0 90.0 90.0 90.0 90.0
R mergeb 0.064 (0.546) 0.140 (0.995) 0.076 (0.578) 0.052 (0.747) 0.075 (0.222) 0.145 (2.032) 0.094 (0.359)
Rpimc 0.041 (0.350) 0.062 (0.445) 0.048 (0.378) 0.022 (0.316) 0.032 (0.094) 0.062 (0.880) 0.040 (0.150)
CC 1/2d 0.997 (0.753) 0.986 (0.776) 0.995 (0.731) 1.000 (0.872) 0.996 (0.977) 0.997 (0.502) 0.995 (0.952)
Redundancy 3.4 (3.4) 6.0 (5.8) 3.5 (3.1) 6.6 (6.5) 6.5 (6.6) 6.5 (6.2) 6.5 (6.7)
Completeness (%) 99.1 (98.6) 99.7 (99.8) 94.5 (87.9) 99.9 (99.3) 100.0 (99.9) 99.8 (99.6) 99.7 (99.7)
I/σ 9.9 (2.0) 7.2 (2.0) 10.1 (1.8) 19.2 (2.2) 15.2 (6.8) 9.8 (1.9) 12.4 (5.6)
Refinement
Resolution (Å) 50.6–1.65 (1.70–1.65) 43.0–1.09 (1.12–1.09) 62.2–1.27 (1.31–1.27) 54.2–1.44 (1.49–1.44) 42.9–1.40 (1.44–1.40) 50.3–1.58 (1.63–1.58) 42.9–1.40 (1.45–1.40)
No. reflections 77846 (7694) 169488 (16796) 162601 (15378) 73857 (7242) 81863 (8131) 106860 (10560) 80865 (7985)
R work/Rfreee 0.187/0.222 (0.267/0.301) 0.183/0.190 (0.275/0.282) 0.182/0.196 (0.264/0.269) 0.174/0.196 (0.258/0.271) 0.166/0.184 (0.195/0.234) 0.184/0.208 (0.252/0.286) 0.152/0.169 (0.166/0.198)
No. atomsf
Protein 5466 2856 5536 2816 2843 5603 2880
Ligand 50 38 50 30 26 90 46
Solvent 193 415 563 266 384 497 432
Average B factors (Å2)
Protein 25 13 17 20 15 19 13
Ligand 29 15 17 22 13 27 22
Solvent 28 25 27 30 27 29 27
R.m.s. deviations
Bond lengths (Å) 0.006 0.004 0.005 0.005 0.004 0.006 0.004
Bond angles (°) 0.81 0.83 0.77 0.80 0.81 0.85 0.82
Ramachandran plotg
Favored 97.04 97.20 96.90 96.35 97.19 96.06 97.19
Allowed 2.96 2.80 3.10 3.65 2.81 3.80 2.81
Outliers 0.00 0.00 0.00 0.00 0.00 0.10 0.00
a

Values in parentheses refer to the highest-resolution shell indicated.

b

Rmerge = ∑hkl∑i|Ii,hkl − ⟨I⟩hkl|/∑hkl∑iIi,hkl, where ⟨I⟩hkl is the average intensity calculated for reflection hkl from replicate measurements.

c

Rp.i.m.= (∑hkl(1/(N-1))1/2∑i|Ii,hkl − ⟨I⟩hkl|)/∑hkl∑i Ii,hkl, where ⟨I⟩hkl is the average intensity calculated for reflection hkl from replicate measurements and N is the number of reflections.

d

Pearson correlation coefficient between random half-datasets.

e

Rwork = ∑||Fo| − |Fc||/∑|Fo| for reflections contained in the working set. |Fo| and |Fc| are the observed and calculated structure factor amplitudes, respectively. Rfree is calculated using the same expression for reflections contained in the test set held aside during refinement.

f

Per asymmetric unit.

g

Calculated with MolProbity.