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Crystal Structure of LC3-p62 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UGM PDB ENTRY 1UGM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 288 0.1M HEPES pH 7.5, 23% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.15 42.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.559 α = 90 b = 39.592 β = 93.3 c = 78.011 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 100 CCD Bruker DIP-6040 2007-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 1.55 77.85 98.4 0.054 23.9 4.5 39943
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.55 1.61 86 0.31 4.2
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 1UGM 1.56 45.48 37918 2005 99.27 0.20281 0.201 0.1993 0.23766 0.238 RANDOM 19.107
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] 0.3 0.71 -0.85 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.241 r_dihedral_angle_4_deg 15.429 r_dihedral_angle_3_deg 11.574 r_dihedral_angle_1_deg 6.218 r_scangle_it 3.557 r_scbond_it 2.283 r_mcangle_it 1.674 r_angle_refined_deg 1.298 r_mcbond_it 1.037 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.241 r_dihedral_angle_4_deg 15.429 r_dihedral_angle_3_deg 11.574 r_dihedral_angle_1_deg 6.218 r_scangle_it 3.557 r_scbond_it 2.283 r_mcangle_it 1.674 r_angle_refined_deg 1.298 r_mcbond_it 1.037 r_nbtor_refined 0.304 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.186 r_symmetry_hbond_refined 0.132 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.096 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 2152 Nucleic Acid Atoms Solvent Atoms 283 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing