☰ Navigation Tabs
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with ITF3756
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 7.5 277 0.1 M Bis-Tris propane pH 7.5, 0.2 M sodium nitrate, 20 % (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.95 38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.483 α = 90 b = 90.753 β = 95.64 c = 71.964 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 EIGER X 16M 2019-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97856 SOLEIL PROXIMA 1
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 1.9 48.25 100 0.176 0.191 0.072 0.996 7.2 7 48867 23.3
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 1.9 1.94 100 1.977 2.136 0.803 0.608 1 6.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5eek 1.9 45.42 46434 2406 99.96 0.1978 0.1946 0.2609 0.2465 RANDOM 32.075
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] 2.98 -2.59 -0.11 -2.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.662 r_dihedral_angle_4_deg 17.651 r_dihedral_angle_3_deg 15.418 r_dihedral_angle_1_deg 7.393 r_angle_refined_deg 1.593 r_angle_other_deg 1.3 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.662 r_dihedral_angle_4_deg 17.651 r_dihedral_angle_3_deg 15.418 r_dihedral_angle_1_deg 7.393 r_angle_refined_deg 1.593 r_angle_other_deg 1.3 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5573 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 139
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction