☰ Navigation Tabs
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with ITF3985
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EEK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.1 M Bis-Tris propane pH 8.5, 0.2 M sodium iodide, 19% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.58 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.966 α = 90 b = 84.212 β = 90 c = 94.977 γ = 90
Symmetry Space Group P 2 21 21
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 2020-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0000 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.3 47.49 91.8 0.255 0.266 0.072 0.996 9.6 13 17684
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 97.4 1.577 1.666 0.524 0.69 9.6
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 5eek 2.3 45.63 16740 895 91.76 0.2025 0.1993 0.2066 0.2599 0.2646 RANDOM 33.176
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] 3.93 -3.91 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.745 r_dihedral_angle_4_deg 17.564 r_dihedral_angle_3_deg 16.195 r_dihedral_angle_1_deg 7.404 r_angle_refined_deg 1.614 r_angle_other_deg 1.317 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.745 r_dihedral_angle_4_deg 17.564 r_dihedral_angle_3_deg 16.195 r_dihedral_angle_1_deg 7.404 r_angle_refined_deg 1.614 r_angle_other_deg 1.317 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2790 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 40
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction