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Crystal structure of Atg13(17BR)-Atg17-Atg29-Atg31 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HPQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 8% PEGMME 5000, 0.1M TrisHCl
Crystal Properties Matthews coefficient Solvent content 5.33 76.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.348 α = 90 b = 63.989 β = 109.25 c = 184.6 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 95 CCD ADSC QUANTUM 210 2013-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 3.2 50 99.9 0.108 8.6 5.6 54575 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.26 100 2.1 5.5
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 4hpq 3.2 44.26 44114 4975 89.68 0.26058 0.25693 0.2477 0.29251 0.2823 RANDOM 92.403
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] 4.95 5.27 1.68 -6.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.854 r_dihedral_angle_3_deg 20.159 r_dihedral_angle_4_deg 17.617 r_long_range_B_refined 12.761 r_long_range_B_other 12.761 r_scangle_other 9.219 r_mcangle_it 8.799 r_mcangle_other 8.798 r_dihedral_angle_1_deg 5.691 r_scbond_it 5.625
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.854 r_dihedral_angle_3_deg 20.159 r_dihedral_angle_4_deg 17.617 r_long_range_B_refined 12.761 r_long_range_B_other 12.761 r_scangle_other 9.219 r_mcangle_it 8.799 r_mcangle_other 8.798 r_dihedral_angle_1_deg 5.691 r_scbond_it 5.625 r_scbond_other 5.624 r_mcbond_it 5.492 r_mcbond_other 5.492 r_angle_refined_deg 1.341 r_angle_other_deg 0.827 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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 8904 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement