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Crystal structure of Danio rerio HDAC6 CD1 and CD2 (linker intact) in complex with Nexturastat A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5G0G PDB ENTRIES 5G0G AND 5G0H experimental model PDB 5G0H PDB ENTRIES 5G0G AND 5G0H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 3.3M SODIUM FORMATE, 17% GLYCEROL, 0.1M TRIS PH 7.5
Crystal Properties Matthews coefficient Solvent content 5.6 78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 187.224 α = 90 b = 187.224 β = 90 c = 102.718 γ = 120
Symmetry Space Group P 32 2 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 6M MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 2.88 162.14 100 0.08 20.4 11.2 47289 -3 88.96
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 2.88 2.89 100 0.79 2.4 11.3
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 PDB ENTRIES 5G0G AND 5G0H 2.88 50 47112 2382 99.96 0.1775 0.1756 0.1871 0.2141 0.2222 RANDOM 90.06
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] -21.9843 -21.9843 43.9685
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.99 t_omega_torsion 2.99 t_angle_deg 1.22 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 19.99 t_omega_torsion 2.99 t_angle_deg 1.22 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 5860 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 33
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing