☰ Navigation Tabs
Deacetylase FI8 utilizes unconventional variant of a catalytic triad: the diluted triad
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AlphaFold2 model with the correct sequence
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 Crystallization condition: 0.3 uL protein solution (9.3 mg/mL protein) and 0.3 uL well solution (0.2 M Ca-acetate, 0.1 M Na-cacodylate pH 6.5, 18% PEG8000). Cryo condition: 0.2 M Ca-acetate, 0.1 M Na-cacodylate, 22% PEG8000, 8% PEG400.
Crystal Properties Matthews coefficient Solvent content 2.85 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.663 α = 90 b = 120.04 β = 90 c = 141.548 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 EIGER X 16M 2022-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.54 50 96.5 0.103 0.107 0.998 12.6 12.5 2930895 -3 31.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.54 1.63 78.4 2.07 2.19 0.396 0.78 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 1.541 48.378 232111 11957 95.955 0.171 0.1697 0.2009 0.2064 30.865
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] -0.956 1.331 -0.374
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.081 r_dihedral_angle_3_deg 12.833 r_dihedral_angle_2_deg 8.995 r_lrange_it 7.675 r_lrange_other 7.576 r_dihedral_angle_1_deg 6.979 r_scangle_it 6.063 r_scangle_other 6.063 r_scbond_it 3.959 r_scbond_other 3.959
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.081 r_dihedral_angle_3_deg 12.833 r_dihedral_angle_2_deg 8.995 r_lrange_it 7.675 r_lrange_other 7.576 r_dihedral_angle_1_deg 6.979 r_scangle_it 6.063 r_scangle_other 6.063 r_scbond_it 3.959 r_scbond_other 3.959 r_mcangle_it 3.283 r_mcangle_other 3.283 r_mcbond_it 2.369 r_mcbond_other 2.369 r_angle_refined_deg 1.813 r_angle_other_deg 0.634 r_nbd_other 0.263 r_symmetry_nbd_refined 0.259 r_nbd_refined 0.218 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.184 r_metal_ion_refined 0.17 r_symmetry_xyhbond_nbd_refined 0.166 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9932 Nucleic Acid Atoms Solvent Atoms 1095 Heterogen Atoms 111
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing