3C0Z

Crystal structure of catalytic domain of human histone deacetylase HDAC7 in complex with SAHA

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	300	20 % PEG 3350, 0.1 M HEPES pH 7.5, 10 % Isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.825	α = 90
b = 81.825	β = 90
c = 148.867	γ = 120

Symmetry
Space Group	P 32

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		2006-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.10000	NSLS	X25

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	2.1	50	93.5	0.049	23.8	3.2	60749	60749

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)
	2.1	2.18	86.4		0.277	3.7	2.3	6428

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	PDB entry 2NVR	2.1	40	57634	3080	93.41	0.19903	0.19664	0.24291	RANDOM	37.023

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]
1.67	0.83		1.67		-2.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.383
r_dihedral_angle_3_deg	18.055
r_dihedral_angle_4_deg	17.684
r_dihedral_angle_1_deg	6.858
r_scangle_it	3.972
r_scbond_it	2.637
r_mcangle_it	1.715
r_angle_refined_deg	1.707
r_mcbond_it	0.996
r_metal_ion_refined	0.338
r_nbtor_refined	0.307
r_symmetry_vdw_refined	0.236
r_nbd_refined	0.225
r_xyhbond_nbd_refined	0.179
r_symmetry_hbond_refined	0.147
r_chiral_restr	0.123
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
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	8400
Nucleic Acid Atoms
Solvent Atoms	332
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing
ARP/wARP	model building