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Crystal Structure of Deacetylase (HdaH) from Vibrio cholerae in complex with SAHA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-A0A395TF31-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 1.4 M sodium acetate
0.1 M MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 1.97 37.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.92 α = 90 b = 81.53 β = 90 c = 133.17 γ = 90
Symmetry Space Group P 21 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 mirror 2024-04-04 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) Rrim 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 47.607 96.9 0.105 0.11 0.999 12.7 11.3 43149
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) 1.9 1.94 81.1 0.756 0.825 0.318 0.911 1.7 5.9
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.9 47.607 43053 2162 96.644 0.178 0.175 0.2403 0.1631 29.447
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] 2.756 0.404 -3.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.605 r_dihedral_angle_6_deg 15.092 r_dihedral_angle_3_deg 13.703 r_lrange_it 8.693 r_lrange_other 8.635 r_dihedral_angle_1_deg 6.973 r_scangle_it 6.278 r_scangle_other 6.277 r_mcangle_other 4.42 r_mcangle_it 4.415
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.605 r_dihedral_angle_6_deg 15.092 r_dihedral_angle_3_deg 13.703 r_lrange_it 8.693 r_lrange_other 8.635 r_dihedral_angle_1_deg 6.973 r_scangle_it 6.278 r_scangle_other 6.277 r_mcangle_other 4.42 r_mcangle_it 4.415 r_scbond_it 4.385 r_scbond_other 4.384 r_mcbond_it 3.213 r_mcbond_other 3.173 r_angle_refined_deg 2.09 r_angle_other_deg 0.719 r_metal_ion_refined 0.28 r_nbd_refined 0.265 r_symmetry_xyhbond_nbd_refined 0.264 r_symmetry_nbd_refined 0.235 r_nbd_other 0.223 r_symmetry_xyhbond_nbd_other 0.221 r_xyhbond_nbd_refined 0.216 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.183 r_chiral_restr 0.101 r_symmetry_nbtor_other 0.085 r_ncsr_local_group_1 0.071 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4817 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing