5KH9

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)
TypeSourceAccession CodeDetails
experimental modelPDB 3C5Kpdbid 3C5K

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62912M Na-formate, 0.2M Na-acetate pH4.6, 5% ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
2.1743.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.434α = 90
b = 44.157β = 90
c = 56.549γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-10-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92819DiamondI04-1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.0734.8199.40.0620.0690.0280.99913.55.546238
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.071.196.60.9571.13.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUTpdbid 3C5K1.0734.844074210499.290.13630.13560.1503RANDOM14.755
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]
-0.75-0.41.15
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free33.838
r_dihedral_angle_2_deg32.088
r_sphericity_bonded16.791
r_dihedral_angle_3_deg11.439
r_dihedral_angle_4_deg8.94
r_dihedral_angle_1_deg6.316
r_rigid_bond_restr2.231
r_mcangle_it1.978
r_angle_refined_deg1.615
r_mcbond_it1.432
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free33.838
r_dihedral_angle_2_deg32.088
r_sphericity_bonded16.791
r_dihedral_angle_3_deg11.439
r_dihedral_angle_4_deg8.94
r_dihedral_angle_1_deg6.316
r_rigid_bond_restr2.231
r_mcangle_it1.978
r_angle_refined_deg1.615
r_mcbond_it1.432
r_mcbond_other1.43
r_angle_other_deg1.111
r_chiral_restr0.114
r_bond_refined_d0.015
r_gen_planes_refined0.012
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms778
Nucleic Acid Atoms
Solvent Atoms79
Heterogen Atoms58

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction