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Crystal structure of Atg13(17BR)-Atg13(17LR)-Atg17-Atg29-Atg31 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4P1W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 5% polyethylene glycol monomethyl ether 5000, 100 mM Tris-HCl
Crystal Properties Matthews coefficient Solvent content 5.2 76.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.956 α = 90 b = 64.043 β = 109.91 c = 184.387 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 RAYONIX MX-225 2013-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 16.3 5.3 53805
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
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 4P1W 3.21 49.22 50369 2700 98.28 0.22596 0.22393 0.2175 0.2651 0.2583 RANDOM 142.453
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] 5.66 7.59 -0.08 -6.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.185 r_dihedral_angle_3_deg 24.037 r_dihedral_angle_4_deg 18.574 r_long_range_B_refined 15.267 r_long_range_B_other 15.267 r_scangle_other 12.184 r_mcangle_it 10.237 r_mcangle_other 10.237 r_scbond_it 7.834 r_scbond_other 7.833
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.185 r_dihedral_angle_3_deg 24.037 r_dihedral_angle_4_deg 18.574 r_long_range_B_refined 15.267 r_long_range_B_other 15.267 r_scangle_other 12.184 r_mcangle_it 10.237 r_mcangle_other 10.237 r_scbond_it 7.834 r_scbond_other 7.833 r_dihedral_angle_1_deg 7.238 r_mcbond_it 6.782 r_mcbond_other 6.782 r_angle_refined_deg 1.726 r_angle_other_deg 1.105 r_chiral_restr 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.003 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 9843 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling