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histone lysine desuccinylase Sirt5 in complex with succinyl peptide H2AK95
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 sodium cacodylate (pH 5.5), 25% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.3 46.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.937 α = 90 b = 42.807 β = 109.25 c = 61.591 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 CCD ADSC QUANTUM 315r 2018-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.9792 SSRF BL17U1
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 1.9 58.15 92.6 0.098 8.9 2.5 19522
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 1.9 1.97 0.302
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 1.92 58.15 18480 1026 91.26 0.17192 0.16893 0.1799 0.22246 0.2218 RANDOM 29.842
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] 0.35 0.27 -0.27 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.028 r_dihedral_angle_4_deg 15.471 r_dihedral_angle_3_deg 14.443 r_long_range_B_other 7.469 r_long_range_B_refined 7.468 r_dihedral_angle_1_deg 6.097 r_scangle_other 5.628 r_scbond_it 3.805 r_scbond_other 3.804 r_angle_other_deg 3.763
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.028 r_dihedral_angle_4_deg 15.471 r_dihedral_angle_3_deg 14.443 r_long_range_B_other 7.469 r_long_range_B_refined 7.468 r_dihedral_angle_1_deg 6.097 r_scangle_other 5.628 r_scbond_it 3.805 r_scbond_other 3.804 r_angle_other_deg 3.763 r_mcangle_it 3.652 r_mcangle_other 3.651 r_mcbond_it 2.656 r_mcbond_other 2.648 r_angle_refined_deg 1.916 r_chiral_restr 0.109 r_gen_planes_other 0.031 r_bond_refined_d 0.018 r_gen_planes_refined 0.014 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 2128 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing