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histone lysine desuccinylase Sirt5 in complex with succinyl peptide H2BK120
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 6.5 295 0.2M Sodium acetate trihydrate, 0.1M Sodium cacodylate trihydrate (pH 6.5), 30%(w/v) PEG8000
Crystal Properties Matthews coefficient Solvent content 2.01 38.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.885 α = 90 b = 64.877 β = 95.92 c = 55.564 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 1.7 55.27 92.3 0.089 15.4 6.9 23736
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 1.7 1.76 0.355
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 1.71 55.27 22645 1079 91.47 0.16353 0.16096 0.169 0.217 0.2225 RANDOM 29.941
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] -1.37 1.12 1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.041 r_dihedral_angle_4_deg 16.251 r_dihedral_angle_3_deg 13.572 r_long_range_B_other 8.146 r_long_range_B_refined 8.144 r_dihedral_angle_1_deg 6.388 r_scangle_other 6.304 r_scbond_it 4.223 r_scbond_other 4.218 r_mcangle_it 3.835
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.041 r_dihedral_angle_4_deg 16.251 r_dihedral_angle_3_deg 13.572 r_long_range_B_other 8.146 r_long_range_B_refined 8.144 r_dihedral_angle_1_deg 6.388 r_scangle_other 6.304 r_scbond_it 4.223 r_scbond_other 4.218 r_mcangle_it 3.835 r_mcangle_other 3.835 r_angle_other_deg 3.742 r_mcbond_it 2.862 r_mcbond_other 2.839 r_angle_refined_deg 2.19 r_chiral_restr 0.139 r_bond_refined_d 0.026 r_gen_planes_other 0.02 r_gen_planes_refined 0.013 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 2123 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing