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Human SIRT2 crystal structure in complex with BHJH-TM1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZGO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 25%(v/v) PEG3350, 0.1M Hepes buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.08 40.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.936 α = 90 b = 116.799 β = 91.77 c = 70.905 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 CCD ADSC QUANTUM 210 2013-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.977 CHESS A1
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 2.1 50 97.7 0.105 9.921 4.5 35229 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 97.3 0.551 0.062 2.385 3.4
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 3ZGO 2.1 45.11 32677 1727 97.66 0.22353 0.22091 0.27332 0.289 RANDOM 46.717
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] -0.98 1.46 -2.34 3.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.465 r_dihedral_angle_4_deg 17.187 r_dihedral_angle_3_deg 16.799 r_long_range_B_refined 6.422 r_long_range_B_other 6.422 r_dihedral_angle_1_deg 6.06 r_scangle_other 4.689 r_mcangle_it 3.722 r_mcangle_other 3.722 r_angle_other_deg 3.594
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.465 r_dihedral_angle_4_deg 17.187 r_dihedral_angle_3_deg 16.799 r_long_range_B_refined 6.422 r_long_range_B_other 6.422 r_dihedral_angle_1_deg 6.06 r_scangle_other 4.689 r_mcangle_it 3.722 r_mcangle_other 3.722 r_angle_other_deg 3.594 r_scbond_it 2.887 r_scbond_other 2.887 r_mcbond_it 2.432 r_mcbond_other 2.43 r_angle_refined_deg 1.241 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_other 0.006 r_gen_planes_refined 0.005 r_bond_other_d 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 4565 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 30
Software Software Software Name Purpose HKL-2000 data collection PHASES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling