3MZ6

Crystal structure of D101L Fe2+ HDAC8 complexed with M344

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.8	298	Drop composition: 25 mM Tris, 2.5% glycerol, 75 mM KCl, 10-18% PEG 35K, 50 mM MES, 1 mM tri(2-carboxyethyl)phosphine (TCEP), 0.03 mM gly-gly-gly, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.616	α = 90
b = 87.561	β = 90
c = 52.488	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	CCD	ADSC QUANTUM 315		2009-04-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	1.0720	APS	24-ID-C

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	50	98.7	0.064	28.1	6.6	53795	28881			36

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	2.07	90.5		0.254	5.2	4.9	2586

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2	50	27381	1457	98.59	0.20225	0.1999	0.24733	RANDOM	32.763

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]
2.62			-0.14		-2.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.72
r_dihedral_angle_4_deg	19.236
r_dihedral_angle_3_deg	15.883
r_dihedral_angle_1_deg	6.397
r_scangle_it	5.58
r_scbond_it	3.547
r_mcangle_it	2.244
r_angle_refined_deg	1.419
r_mcbond_it	1.327
r_chiral_restr	0.109
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2784
Nucleic Acid Atoms
Solvent Atoms	156
Heterogen Atoms	25

Software

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