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Sirtuin 4 from Xenopus tropicalis in complex with thioacetyl-ADP-ribose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OJ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 0.5 M Na/K-tartrate
0.5% PEG5000MME
0.1 M Tris
Crystal Properties Matthews coefficient Solvent content 2.2 44.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.97 α = 90 b = 74.88 β = 90 c = 109.55 γ = 90
Symmetry Space Group C 2 2 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 PILATUS 6M Sagitally bended Si111-crystal 2015-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.976250 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.8 20 99.7 0.055 0.999 18.3 6.8 26585
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 99.9 1.04 0.704 2.1 7.1
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 5OJ7 1.8 19.74 25255 1330 99.74 0.15787 0.15528 0.1656 0.20883 0.2147 RANDOM 38.417
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] -0.62 1.27 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.154 r_dihedral_angle_4_deg 14.717 r_dihedral_angle_3_deg 14.372 r_long_range_B_refined 7.856 r_long_range_B_other 7.854 r_scangle_other 6.428 r_dihedral_angle_1_deg 6.371 r_scbond_other 4.313 r_scbond_it 4.309 r_mcangle_it 3.728
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.154 r_dihedral_angle_4_deg 14.717 r_dihedral_angle_3_deg 14.372 r_long_range_B_refined 7.856 r_long_range_B_other 7.854 r_scangle_other 6.428 r_dihedral_angle_1_deg 6.371 r_scbond_other 4.313 r_scbond_it 4.309 r_mcangle_it 3.728 r_mcangle_other 3.727 r_mcbond_other 2.753 r_mcbond_it 2.752 r_angle_refined_deg 2.438 r_angle_other_deg 1.26 r_chiral_restr 0.162 r_bond_refined_d 0.029 r_gen_planes_refined 0.014 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2153 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing