5KH9 | pdb_00005kh9

Crystal structure of a low occupancy fragment candidate (5-[(4-Isopropylphenyl)amino]-6-methyl-1,2,4-triazin-3(2H)-one) 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	3C5K	pdbid 3C5K

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.434	α = 90
b = 44.157	β = 90
c = 56.549	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	PIXEL	DECTRIS PILATUS 6M-F		2015-10-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92819	Diamond	I04-1

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	1.07	34.81	99.4	0.062	0.069	0.028	0.999	13.5	5.5		46238

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)
1	1.07	1.1	96.6		0.957	1.1	3.1

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 3C5K	1.07	34.8	44074	2104	99.29	0.1363	0.1356	0.15	0.1503	0.16	RANDOM	14.755

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]
-0.75			-0.4		1.15

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	33.838
r_dihedral_angle_2_deg	32.088
r_sphericity_bonded	16.791
r_dihedral_angle_3_deg	11.439
r_dihedral_angle_4_deg	8.94
r_dihedral_angle_1_deg	6.316
r_rigid_bond_restr	2.231
r_mcangle_it	1.978
r_angle_refined_deg	1.615
r_mcbond_it	1.432

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	33.838
r_dihedral_angle_2_deg	32.088
r_sphericity_bonded	16.791
r_dihedral_angle_3_deg	11.439
r_dihedral_angle_4_deg	8.94
r_dihedral_angle_1_deg	6.316
r_rigid_bond_restr	2.231
r_mcangle_it	1.978
r_angle_refined_deg	1.615
r_mcbond_it	1.432
r_mcbond_other	1.43
r_angle_other_deg	1.111
r_chiral_restr	0.114
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	778
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms	58

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	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.