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Human SIRT2 in complex with myristoylated peptide (TNF-alphaK20myr)
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 3350
Crystal Properties Matthews coefficient Solvent content 2.33 47.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.136 α = 101.07 b = 48.785 β = 91.33 c = 96.96 γ = 112.27
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 315 2014-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
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 1.6 50 95.7 0.049 14.3 1.9 77514
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 1J8F, 3ZGO 1.6 20 73362 3770 95 0.20769 0.20631 0.2061 0.23457 0.2343 RANDOM 16.931
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] -0.02 -0.01 -0.04 -0.13 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.113 r_dihedral_angle_4_deg 15.551 r_dihedral_angle_3_deg 13.304 r_dihedral_angle_1_deg 5.421 r_long_range_B_refined 3.823 r_angle_refined_deg 1.215 r_mcangle_it 1.129 r_scbond_it 0.662 r_mcbond_it 0.629 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.113 r_dihedral_angle_4_deg 15.551 r_dihedral_angle_3_deg 13.304 r_dihedral_angle_1_deg 5.421 r_long_range_B_refined 3.823 r_angle_refined_deg 1.215 r_mcangle_it 1.129 r_scbond_it 0.662 r_mcbond_it 0.629 r_chiral_restr 0.082 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 4551 Nucleic Acid Atoms Solvent Atoms 424 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing