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Crystal structure of human HDAC6 in complex with ubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C5K PDB entry 3C5K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 297 15% PEG 3350, 0.1M Ammonium Sulphate, 0.1M Bis-Tris, pH 5.6, temperature 297K
Crystal Properties Matthews coefficient Solvent content 3.22 61.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.748 α = 90 b = 133.748 β = 90 c = 118.768 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD MARMOSAIC 300 mm CCD 2008-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03317 APS 23-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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3 50 100 0.091 0.091 45.8 16.2 22204 22204 92.68
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.05 100 0.767 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3C5K 3 32.72 22135 22135 463 0.2352 0.2352 0.2346 0.2496 0.2648 0.2838 RANDOM 72.86
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 -3.4578 6.9157
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.83 t_omega_torsion 3.88 t_angle_deg 1.12 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.83 t_omega_torsion 3.88 t_angle_deg 1.12 t_bond_d 0.01 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 Atoms Number Protein Atoms 3307 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 12
Software Software Software Name Purpose Blu-Ice data collection MOLREP phasing BUSTER refinement Coot model building HKL-2000 data reduction HKL-2000 data scaling