3EWF

Crystal Structure Analysis of human HDAC8 H143A variant complexed with substrate.

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2V5W	PDB entry 2V5W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	Reservoir solution: 50 mM Tris-HCl, 50 mM MgCl2, 150 mM KCl, 13% PEG 6000, 2 mM TCEP. Enzyme was incubated with 3.2 mM substrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.903	α = 90
b = 91.844	β = 90
c = 196.577	γ = 90

Symmetry
Space Group	P 21 21 21

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 315		2008-07-10	M	SINGLE WAVELENGTH
2	1	x-ray		CCD	ADSC QUANTUM 315		2008-07-10

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97926	APS	24-ID-C
2	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.97920	APS	24-ID-E

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	2.5	50	99.4	0.137	11.8	7.2	52790	52790			22.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.5	2.59	95.2		0.517	1.8	4.2

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-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2V5W	2.5	49.15	52790	49380	4032	93.6	0.198	0.198	0.229	RANDOM	30.3

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]
7.85			-8.43		0.57

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.7
c_angle_deg	1.3
c_improper_angle_d	0.76
c_bond_d	0.008
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11528
Nucleic Acid Atoms
Solvent Atoms	299
Heterogen Atoms	66

Software

Software
Software Name	Purpose
CBASS	data collection
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling