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histone lysine desuccinylase Sirt5 in complex with succinyl peptide H4K91
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ACE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 295 0.1 M BIS-TRIS (pH 5.5), 25% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.23 44.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.078 α = 90 b = 41.267 β = 108.37 c = 61.334 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 6M 2018-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9793 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.3 58.21 99 0.149 8.5 5.1 12138
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 0.412
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6ACE 2.3 58.21 11320 623 98.92 0.20721 0.20327 0.2078 0.2851 0.2938 RANDOM 69.033
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] -1.27 1.36 4.22 -3.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.14 r_dihedral_angle_4_deg 22.707 r_dihedral_angle_3_deg 15.254 r_long_range_B_refined 12.132 r_long_range_B_other 12.13 r_scangle_other 9.43 r_mcangle_it 7.936 r_mcangle_other 7.933 r_dihedral_angle_1_deg 6.643 r_scbond_it 6.351
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.14 r_dihedral_angle_4_deg 22.707 r_dihedral_angle_3_deg 15.254 r_long_range_B_refined 12.132 r_long_range_B_other 12.13 r_scangle_other 9.43 r_mcangle_it 7.936 r_mcangle_other 7.933 r_dihedral_angle_1_deg 6.643 r_scbond_it 6.351 r_scbond_other 6.348 r_mcbond_it 5.561 r_mcbond_other 5.56 r_angle_other_deg 3.729 r_angle_refined_deg 1.664 r_chiral_restr 0.095 r_bond_refined_d 0.092 r_gen_planes_other 0.012 r_gen_planes_refined 0.011 r_bond_other_d 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2098 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing