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X-ray structure of Leptospira interrogans Histone deacetylase 11 (HDAC11) in complex with cis-5-dodecenoic acid.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 1 protein:2 precipitant
100 mM HEPES pH 7.4,
200 mM MgCl2,
23% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.07 40.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.265 α = 90 b = 61.744 β = 99.86 c = 49.481 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 PILATUS3 S 6M 2023-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.55 48.75 98.7 0.116 0.048 0.997 13 6.6 40698
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.58 91.2 1.681 0.621 0.451 1.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.55 48.75 38658 2020 98.58 0.17438 0.17295 0.1729 0.20071 0.2006 RANDOM 21.427
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] 0.65 -0.58 -0.74 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.25 r_dihedral_angle_3_deg 13.928 r_dihedral_angle_4_deg 10.342 r_dihedral_angle_1_deg 6.404 r_long_range_B_refined 4.829 r_scbond_it 2.304 r_mcangle_it 1.824 r_angle_refined_deg 1.474 r_mcbond_it 1.269 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.25 r_dihedral_angle_3_deg 13.928 r_dihedral_angle_4_deg 10.342 r_dihedral_angle_1_deg 6.404 r_long_range_B_refined 4.829 r_scbond_it 2.304 r_mcangle_it 1.824 r_angle_refined_deg 1.474 r_mcbond_it 1.269 r_chiral_restr 0.109 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2450 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction Auto-Rickshaw phasing