3GV4

Crystal structure of human HDAC6 zinc finger domain and ubiquitin C-terminal peptide RLRGG


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3C5KPDB entry 3C5K

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29720% PEG3350, 0.2 M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
2.0239.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.657α = 90
b = 36.093β = 90
c = 88.998γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++VariMax HR2008-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
11.725094.50.0730.07314.15.8108651086522.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.721.7872.50.2310.2314.263.1813

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3C5K1.7233.45102131021360994.640.176950.176950.173820.23034RANDOM21.958
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]
0.01-1.311.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.527
r_dihedral_angle_4_deg16.224
r_dihedral_angle_3_deg11.322
r_dihedral_angle_1_deg5.813
r_scangle_it2.47
r_scbond_it1.595
r_angle_refined_deg1.191
r_mcangle_it1.02
r_mcbond_it0.612
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.527
r_dihedral_angle_4_deg16.224
r_dihedral_angle_3_deg11.322
r_dihedral_angle_1_deg5.813
r_scangle_it2.47
r_scbond_it1.595
r_angle_refined_deg1.191
r_mcangle_it1.02
r_mcbond_it0.612
r_nbtor_refined0.303
r_symmetry_vdw_refined0.208
r_nbd_refined0.193
r_symmetry_hbond_refined0.162
r_xyhbond_nbd_refined0.153
r_chiral_restr0.093
r_symmetry_metal_ion_refined0.039
r_metal_ion_refined0.037
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms799
Nucleic Acid Atoms
Solvent Atoms205
Heterogen Atoms4

Software

Software
Software NamePurpose
SBC-Collectdata collection
PHASESphasing
REFMACrefinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling