☰ Navigation Tabs
Crystal structure of autophagy-related protein Atg8 from the silkworm Bombyx mori
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KJT PDB ENTRY 1KJT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 289 2.0M Ammonium Sulfate, 0.1M Sodium Citrate, 0.2M Sodium/Potassium Tartrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.47 64.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.768 α = 90 b = 96.768 β = 90 c = 44.309 γ = 90
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 2009-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 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 2.4 96.7 89.6 0.083 14.4 14385 14385
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.4 2.49 86.8
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 PDB ENTRY 1KJT 2.4 27.08 14385 765 92.63 0.23329 0.23112 0.2336 0.27309 0.2685 RANDOM 48.688
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] 0.19 0.19 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.567 r_dihedral_angle_3_deg 21.687 r_dihedral_angle_4_deg 21.318 r_dihedral_angle_1_deg 7.638 r_scangle_it 4.419 r_mcangle_it 3.303 r_scbond_it 2.821 r_mcbond_it 2.028 r_angle_refined_deg 1.941 r_chiral_restr 0.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.567 r_dihedral_angle_3_deg 21.687 r_dihedral_angle_4_deg 21.318 r_dihedral_angle_1_deg 7.638 r_scangle_it 4.419 r_mcangle_it 3.303 r_scbond_it 2.821 r_mcbond_it 2.028 r_angle_refined_deg 1.941 r_chiral_restr 0.155 r_bond_refined_d 0.024 r_gen_planes_refined 0.009 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1950 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling