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Human SIRT2 in complex with 2-O-myristoyl-ADP-ribose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J8F 1J8F, 3ZGO experimental model PDB 3ZGO 1J8F, 3ZGO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG 2000
Crystal Properties Matthews coefficient Solvent content 2.09 41.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.186 α = 90 b = 142.369 β = 94.41 c = 62.626 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 PIXEL DECTRIS PILATUS 6M 2014-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 20 98.3 0.063 17 3.4 90675
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 1J8F, 3ZGO 1.9 20 74580 3901 93.6 0.233 0.231 0.267 0.2795 RANDOM 22.28
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] 0.06 0.1 0.15 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.326 r_dihedral_angle_3_deg 15.639 r_dihedral_angle_4_deg 14.379 r_dihedral_angle_1_deg 6.097 r_long_range_B_refined 3.183 r_long_range_B_other 3.139 r_mcangle_it 1.832 r_mcangle_other 1.832 r_scangle_other 1.816 r_angle_refined_deg 1.414
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.326 r_dihedral_angle_3_deg 15.639 r_dihedral_angle_4_deg 14.379 r_dihedral_angle_1_deg 6.097 r_long_range_B_refined 3.183 r_long_range_B_other 3.139 r_mcangle_it 1.832 r_mcangle_other 1.832 r_scangle_other 1.816 r_angle_refined_deg 1.414 r_scbond_it 1.087 r_scbond_other 1.087 r_mcbond_it 1.078 r_mcbond_other 1.077 r_angle_other_deg 1.014 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_bond_other_d 0.006 r_gen_planes_refined 0.004 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 9020 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 200
Software Software Software Name Purpose REFMAC refinement