5B8D

Crystal structure of a low occupancy fragment candidate (N-(4-Methyl-1,3-thiazol-2-yl)propanamide) bound adjacent to 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-F2015-09-30MSINGLE 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
11.0534.897.40.0580.0640.0260.99914.65.447523
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)RedundancyNumber Unique Reflections (All)
11.051.0779.10.8931.1250.6720.47812.41876

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 3C5K1.0534.845286217897.20.12910.12830.1464RANDOM13.189
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]
-0.210.67-0.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.21
r_sphericity_free20.677
r_dihedral_angle_3_deg11.047
r_dihedral_angle_1_deg6.624
r_dihedral_angle_4_deg6.14
r_sphericity_bonded5.867
r_rigid_bond_restr1.543
r_angle_refined_deg1.504
r_mcangle_it1.177
r_angle_other_deg1.098
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.21
r_sphericity_free20.677
r_dihedral_angle_3_deg11.047
r_dihedral_angle_1_deg6.624
r_dihedral_angle_4_deg6.14
r_sphericity_bonded5.867
r_rigid_bond_restr1.543
r_angle_refined_deg1.504
r_mcangle_it1.177
r_angle_other_deg1.098
r_mcbond_other0.886
r_mcbond_it0.862
r_chiral_restr0.11
r_bond_refined_d0.016
r_gen_planes_refined0.01
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms779
Nucleic Acid Atoms
Solvent Atoms79
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction