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Crystal structure of human Sirt2 in complex with ADPR and EX-243
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5D7O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.75 293 18 % (w/v) PEG 10000, 0.1 M Bis-Tris
Crystal Properties Matthews coefficient Solvent content 2.46 50.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.496 α = 90 b = 77.578 β = 90 c = 114.206 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 IMAGE PLATE MAR scanner 345 mm plate 2013-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 1.76 39.41 97.8 0.08 18.9 14.3 66454
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 1.76 1.79 1.136
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 5D7O 1.76 39.41 63026 3367 97.59 0.19182 0.1901 0.198 0.22444 0.2296 RANDOM 34.863
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] 1.62 -0.44 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.387 r_dihedral_angle_4_deg 14.582 r_dihedral_angle_3_deg 13.136 r_dihedral_angle_1_deg 5.706 r_long_range_B_refined 4.53 r_long_range_B_other 4.465 r_scangle_other 2.55 r_mcangle_it 2.103 r_mcangle_other 2.103 r_scbond_it 1.514
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.387 r_dihedral_angle_4_deg 14.582 r_dihedral_angle_3_deg 13.136 r_dihedral_angle_1_deg 5.706 r_long_range_B_refined 4.53 r_long_range_B_other 4.465 r_scangle_other 2.55 r_mcangle_it 2.103 r_mcangle_other 2.103 r_scbond_it 1.514 r_scbond_other 1.514 r_angle_refined_deg 1.34 r_mcbond_it 1.296 r_mcbond_other 1.295 r_angle_other_deg 0.791 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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 4775 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 149
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing