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Human SIRT2 in complex with myristoylated peptide (H3K9myr)
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 47.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.102 α = 101.05 b = 48.824 β = 91.53 c = 97.147 γ = 112.07
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 1.00 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 95.6 0.023 38.5 3.9 79168
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 74836 3849 96.65 0.20832 0.20712 0.2068 0.23241 0.2322 RANDOM 16.193
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] 0.04 -0.04 0.04 -0.08 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.496 r_dihedral_angle_4_deg 14.625 r_dihedral_angle_3_deg 13.265 r_dihedral_angle_1_deg 5.325 r_long_range_B_refined 3.811 r_angle_refined_deg 1.217 r_mcangle_it 1.152 r_scbond_it 0.659 r_mcbond_it 0.639 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.496 r_dihedral_angle_4_deg 14.625 r_dihedral_angle_3_deg 13.265 r_dihedral_angle_1_deg 5.325 r_long_range_B_refined 3.811 r_angle_refined_deg 1.217 r_mcangle_it 1.152 r_scbond_it 0.659 r_mcbond_it 0.639 r_chiral_restr 0.083 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 4533 Nucleic Acid Atoms Solvent Atoms 522 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing