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Crystal structure of the ADP-ribosylating sirtuin (SirTM) from Streptococcus pyogenes (Apo form)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 0.1 M AMINO ACIDS, 0.1 M BUFFER SYSTEM 1 (PH 6.5), 30.00% (V/V) EDO_P8K (THESE ARE COMPONENTS OF THE MORPHEUS SCREEN FROM MOLECULAR DIMENSIONS)
Crystal Properties Matthews coefficient Solvent content 2.14 43.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.16 α = 99.87 b = 41.51 β = 94.63 c = 51.23 γ = 90.77
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 2M TORROIDAL MIRROR 2014-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 1.54 34.81 88.3 0.06 10.6 3.8 36095
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 1.54 1.58 82.8 0.55 2 3.8
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 SAD THROUGHOUT NONE 1.54 34.81 34287 1808 88.28 0.15205 0.14956 0.1628 0.19998 0.2118 RANDOM 19.183
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] -0.05 -0.39 -0.57 0.95 -0.04 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.581 r_dihedral_angle_3_deg 13.765 r_dihedral_angle_4_deg 13.279 r_dihedral_angle_1_deg 6.183 r_scangle_it 3.595 r_mcangle_it 2.307 r_scbond_it 2.265 r_mcbond_it 1.593 r_mcbond_other 1.506 r_angle_refined_deg 1.421
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.581 r_dihedral_angle_3_deg 13.765 r_dihedral_angle_4_deg 13.279 r_dihedral_angle_1_deg 6.183 r_scangle_it 3.595 r_mcangle_it 2.307 r_scbond_it 2.265 r_mcbond_it 1.593 r_mcbond_other 1.506 r_angle_refined_deg 1.421 r_angle_other_deg 0.786 r_chiral_restr 0.099 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2345 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling autoSHARP phasing