6ODC

Crystal structure of HDAC8 in complex with compound 30

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.3	291	0.1M MES pH5.3, 5% PEG6000, 0.14 M Gly-Gly-Gly, 2mM TCEP

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.54	α = 90
b = 91.161	β = 94.07
c = 92.574	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r		2017-01-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.99	SSRF	BL18U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.8	50	99.8	0.0125	14.8	3.4		35823

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.9	99.9		1.5	3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1t64	2.8	50	34035	1768	99.11	0.19642	0.1944	0.23577	RANDOM	76.315

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
4.14		-3.68	-0.92		-2.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.546
r_dihedral_angle_3_deg	15.924
r_dihedral_angle_4_deg	13.926
r_long_range_B_other	10.956
r_long_range_B_refined	10.951
r_scangle_other	8.018
r_mcangle_other	7.797
r_mcangle_it	7.792
r_dihedral_angle_1_deg	6.354
r_mcbond_it	5.164
r_scbond_it	5.158
r_scbond_other	5.157
r_mcbond_other	5.143
r_angle_refined_deg	1.452
r_angle_other_deg	0.966
r_chiral_restr	0.078
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8476
Nucleic Acid Atoms
Solvent Atoms	59
Heterogen Atoms	100

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing