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Crystal structure of Sirt2-ADPR at an improved resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZGV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.25 277 0.2 M sodium chloride, 30 % (w/v) PEG 3350, 0.1 M Bis-Tris
Crystal Properties Matthews coefficient Solvent content 2.49 50.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78 α = 90 b = 78.17 β = 90 c = 114.241 γ = 90
Symmetry Space Group P 21 21 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 2013-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1 SLS X06SA
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 1.63 49.71 100 0.114 8 6.1 87718
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 1.63 1.66 0.983
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3ZGV 1.63 49.71 83210 4433 99.45 0.17192 0.17088 0.1907 0.2088 RANDOM 27.975
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] 1.04 2.73 -3.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.016 r_dihedral_angle_3_deg 13.542 r_dihedral_angle_4_deg 11.922 r_dihedral_angle_1_deg 5.227 r_long_range_B_refined 3.057 r_long_range_B_other 3.057 r_mcangle_it 1.449 r_mcangle_other 1.449 r_scangle_other 1.237 r_angle_refined_deg 1.149
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.016 r_dihedral_angle_3_deg 13.542 r_dihedral_angle_4_deg 11.922 r_dihedral_angle_1_deg 5.227 r_long_range_B_refined 3.057 r_long_range_B_other 3.057 r_mcangle_it 1.449 r_mcangle_other 1.449 r_scangle_other 1.237 r_angle_refined_deg 1.149 r_mcbond_it 0.817 r_mcbond_other 0.817 r_angle_other_deg 0.741 r_scbond_it 0.722 r_scbond_other 0.722 r_chiral_restr 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 4766 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement MOLREP phasing Aimless data scaling MOSFLM data reduction