5KH7

Crystal structure of fragment (3-[6-Oxo-3-(3-pyridinyl)-1(6H)-pyridazinyl]propanoic acid) 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
2.0941.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.719α = 90
b = 43.776β = 90
c = 55.924γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN A2002016-05-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.54178

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.634.4799.90.030.0330.012143.56.713752
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)
11.61.6399.60.0930.1010.0390.99518.26.4678

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 3C5K1.734.471093254499.920.14790.14610.1827RANDOM9.628
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]
-0.010.49-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.966
r_dihedral_angle_4_deg15.452
r_dihedral_angle_3_deg11.206
r_dihedral_angle_1_deg6.388
r_angle_refined_deg1.489
r_mcangle_it1.237
r_angle_other_deg1.068
r_mcbond_it0.74
r_mcbond_other0.74
r_chiral_restr0.111
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.966
r_dihedral_angle_4_deg15.452
r_dihedral_angle_3_deg11.206
r_dihedral_angle_1_deg6.388
r_angle_refined_deg1.489
r_mcangle_it1.237
r_angle_other_deg1.068
r_mcbond_it0.74
r_mcbond_other0.74
r_chiral_restr0.111
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms779
Nucleic Acid Atoms
Solvent Atoms117
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction