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X-ray structure of Leptospira interrogans Histone deacetylase 11 (HDAC11) in complex with cis-dodec-5-enoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 5:1:5
Precipitant: 0.1 M CaCl2, 0.1 M MgCl2, 0.1 M PIPES pH 7.0, 5.625% PEG 3350, 5.625% PEG 4000, 5.625% PEG 2000, 5.625% PEG 5000 MME
Seeding stock
0.1 M HEPES pH 7.4, 0.1 M MgCl2, 0.1 M NaCl, 25% (w/v) PEG 3350
Protein in buffer: 25 mM Tris-HCl, 140 mM NaCl, 100 mM KCl, 3% glycerol, pH 8
cryoprotection: 25% glycerol in precipitant
Crystal Properties Matthews coefficient Solvent content 2.14 42.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.739 α = 88.49 b = 50.366 β = 89.97 c = 62.175 γ = 79.72
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 2023-01-20 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) 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 1.51 49.54 90 0.058 0.998 14.1 3.7 83014
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.51 1.53 56.8 0.518 0.785 2.4 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 1.51 32.19 1.98 83005 4119 89.97 0.1575 0.1561 0.1568 0.1841 0.1842 random selection
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.817 f_angle_d 0.833 f_chiral_restr 0.054 f_plane_restr 0.006 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4908 Nucleic Acid Atoms Solvent Atoms 522 Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling Auto-Rickshaw phasing