☰ Navigation Tabs
Zebrafish Sirt5 in complex with stalled bicyclic intermediate of inhibitory compound 10
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UTV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 20% PEG8000
0.2 M MgCl2
0.1 M Tris/HCl pH 8.5
0.1 M Glycine
Crystal Properties Matthews coefficient Solvent content 2.36 47.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.47 α = 90 b = 38.25 β = 122.51 c = 75.55 γ = 90
Symmetry Space Group C 1 2 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 2M-F 2016-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.000030 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 1.95 50 99.1 0.213 0.989 6.8 4.1 20704
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 99.2 1.565 0.463 1.1 4.1
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 4UTV 1.95 49.11 19704 1037 99.62 0.19706 0.19467 0.24169 0.2188 RANDOM 26.588
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] -1.18 0.21 0.12 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.337 r_dihedral_angle_4_deg 18.355 r_dihedral_angle_3_deg 16.058 r_dihedral_angle_1_deg 6.2 r_long_range_B_refined 5.529 r_long_range_B_other 5.528 r_scangle_other 4.183 r_mcangle_it 2.731 r_mcangle_other 2.73 r_scbond_other 2.693
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.337 r_dihedral_angle_4_deg 18.355 r_dihedral_angle_3_deg 16.058 r_dihedral_angle_1_deg 6.2 r_long_range_B_refined 5.529 r_long_range_B_other 5.528 r_scangle_other 4.183 r_mcangle_it 2.731 r_mcangle_other 2.73 r_scbond_other 2.693 r_scbond_it 2.691 r_angle_refined_deg 1.971 r_mcbond_it 1.91 r_mcbond_other 1.91 r_angle_other_deg 1.162 r_chiral_restr 0.115 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 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 2072 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing