3PHD

Crystal structure of human HDAC6 in complex with ubiquitin


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.629715% PEG 3350, 0.1M Ammonium Sulphate, 0.1M Bis-Tris, pH 5.6, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
3.2261.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 133.748α = 90
b = 133.748β = 90
c = 118.768γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMARMOSAIC 300 mm CCD2008-03-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.03317APS23-ID-B

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
13501000.0910.09145.816.2222042220492.68
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)
133.051000.7674.7

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 3C5K332.7222135221354630.23520.23520.23460.2648RANDOM72.86
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]
-3.4578-3.45786.9157
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion19.83
t_omega_torsion3.88
t_angle_deg1.12
t_bond_d0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion19.83
t_omega_torsion3.88
t_angle_deg1.12
t_bond_d0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3307
Nucleic Acid Atoms
Solvent Atoms2
Heterogen Atoms12

Software

Software
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
BUSTERrefinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling