3GV4

Crystal structure of human HDAC6 zinc finger domain and ubiquitin C-terminal peptide RLRGG

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3C5K	PDB entry 3C5K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		297	20% PEG3350, 0.2 M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.657	α = 90
b = 36.093	β = 90
c = 88.998	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	IMAGE PLATE	RIGAKU RAXIS IV++	VariMax HR	2008-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.54

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	1.72	50	94.5	0.073	0.073	14.1	5.8	10865	10865			22.9

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)
	1.72	1.78	72.5		0.231	0.231	4.26	3.1	813

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3C5K	1.72	33.45	10213	10213	609	94.64	0.17695	0.17695	0.17382	0.23034	RANDOM	21.958

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]
0.01			-1.31		1.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.527
r_dihedral_angle_4_deg	16.224
r_dihedral_angle_3_deg	11.322
r_dihedral_angle_1_deg	5.813
r_scangle_it	2.47
r_scbond_it	1.595
r_angle_refined_deg	1.191
r_mcangle_it	1.02
r_mcbond_it	0.612
r_nbtor_refined	0.303
r_symmetry_vdw_refined	0.208
r_nbd_refined	0.193
r_symmetry_hbond_refined	0.162
r_xyhbond_nbd_refined	0.153
r_chiral_restr	0.093
r_symmetry_metal_ion_refined	0.039
r_metal_ion_refined	0.037
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
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_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	799
Nucleic Acid Atoms
Solvent Atoms	205
Heterogen Atoms	4

Software

Software
Software Name	Purpose
SBC-Collect	data collection
PHASES	phasing
REFMAC	refinement
Coot	model building
HKL-2000	data reduction
HKL-2000	data scaling