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Crystal structure of Danio rerio HDAC6 CD2 in complex with (S)- trichostatin A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other HOMOLOGY MODEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 15% PEG 3350, 0.1M KCL
Crystal Properties Matthews coefficient Solvent content 1.8 32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.98 α = 90 b = 48.23 β = 103.22 c = 73.78 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.6 50 96.7 0.08 10.2 3.2 44152 -3 18.31
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 1.6 1.64 83.8 0.71 1.6 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 HOMOLOGY MODEL 1.6 23.43 44079 2204 97.22 0.1515 0.1502 0.1566 0.1741 0.185 RANDOM 20.62
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] -7.0782 -3.2574 3.2915 3.7866
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.85 t_omega_torsion 3.87 t_angle_deg 0.99 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 14.85 t_omega_torsion 3.87 t_angle_deg 0.99 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 2810 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 65
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing