6CEE | pdb_00006cee

Crystal structure of fragment 3-(1-Methyl-2-oxo-1,2-dihydroquinoxalin-3-yl)propionic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5KH3	pdbid 5KH3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	291	2 M Na-formate, 0.2 M Na-acetate pH4.6, 5 % ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.72	α = 90
b = 44.11	β = 90
c = 55.91	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	RIGAKU SATURN A200		2017-08-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.55	30	100	0.037	0.04	0.015	1	40.5	6.7		15166

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.58	100		0.231	0.253	0.102	0.967		6

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	pdbid 5KH3	1.55	30	14437	728	99.89	0.1538	0.153	0.17	0.1694	0.18	RANDOM	12.359

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]
-0.05			0.7		-0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.633
r_dihedral_angle_4_deg	23.323
r_dihedral_angle_3_deg	11.994
r_dihedral_angle_1_deg	6.585
r_angle_refined_deg	1.675
r_angle_other_deg	1.172
r_chiral_restr	0.124
r_bond_refined_d	0.015
r_gen_planes_refined	0.011
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.633
r_dihedral_angle_4_deg	23.323
r_dihedral_angle_3_deg	11.994
r_dihedral_angle_1_deg	6.585
r_angle_refined_deg	1.675
r_angle_other_deg	1.172
r_chiral_restr	0.124
r_bond_refined_d	0.015
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	777
Nucleic Acid Atoms
Solvent Atoms	87
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.