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LC3A in complex with (3R,4S,5R,6R)-5-hydroxy-6-((4-hydroxy-3-(4-hydroxy-3-isopentylbenzamido)-8-methyl-2-oxo-2H-chromen-7-yl)oxy)-3-methoxy-2,2-dimethyltetrahydro-2H-pyran-4-yl carbamate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WAL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.2 M ammoniumnitrat and 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.83 56.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.738 α = 90 b = 95.738 β = 90 c = 34.647 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 PIXEL DECTRIS EIGER X 16M 2019-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.99987 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.67 47.869 98.39 0.04498 0.04686 0.01285 0.978 32.19 13.8 18199 26.9789688009
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.67 1.79 97.5 0.615 0.661 0.874 2.8 7.305
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 3WAL 1.67008040045 47.869 1.3740483431 18199 1749 98.2911729277 0.187369648755 0.186062076115 0.1897 0.212197763923 0.2219 Random selection 36.9637307029
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 26.0043791132 f_angle_d 0.988272062334 f_chiral_restr 0.0552765735278 f_bond_d 0.0109421031014 f_plane_restr 0.00512313268387
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 959 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 52
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing