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Crystal structure of human SIRT5 in XR-0931
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8GBL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 23%-27% (v/v) PEG 3350, 0.1 M MES, pH 5.5-6.0, 0.1-0.2 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.3 46.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.753 α = 90 b = 56.13 β = 89.97 c = 114.713 γ = 90
Symmetry Space Group P 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 195 PIXEL DECTRIS PILATUS3 X CdTe 1M 2025-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 1.0000 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.24 50 99.7 0.762 10.86 6.37 25615
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.24 2.3 0.0025
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.242 41.753 1.36 25610 2010 99.55 0.1882 0.1827 0.1854 0.2528 0.256
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 15.621 f_angle_d 1.818 f_chiral_restr 0.072 f_bond_d 0.016 f_plane_restr 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3824 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 92
Software Software Software Name Purpose PHENIX refinement autoPX data processing autoPX data reduction PHASER phasing PDB_EXTRACT data extraction