1T69

Crystal Structure of human HDAC8 complexed with SAHA

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.6	277	PEG 8000, HEPES, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.761	α = 90
b = 80.761	β = 90
c = 105.615	γ = 120

Symmetry
Space Group	P 31 2 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 4	mirrors	2001-05-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	1.0	ALS	5.0.3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.9	70	95	0.076	0.076	17	5.3	8595	8164			68

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.9	3	96.5		0.54	0.54	4	5	870

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1T67	2.91	70.71	8595	8164	406	94.14	0.24926	0.31027	RANDOM	68.095

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]
2.75	1.38		2.75		-4.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.099
r_scangle_it	1.736
r_angle_refined_deg	1.281
r_scbond_it	1.014
r_mcangle_it	0.836
r_symmetry_hbond_refined	0.458
r_mcbond_it	0.439
r_nbd_refined	0.215
r_symmetry_vdw_refined	0.202
r_xyhbond_nbd_refined	0.158
r_chiral_restr	0.085
r_metal_ion_refined	0.08
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2737
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	20

Software

Software
Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction