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Crystal structure of truncated human Microtubule-associated proteins 1A/1B light chain 3B (MAP1LC3B) in apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5D94
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.7 293 36% PEG 8000, 0.1M acetate pH 4.7
Crystal Properties Matthews coefficient Solvent content 2.14 42.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.255 α = 90 b = 60.255 β = 90 c = 34.927 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 2022-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.99999 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 1.36 42.61 97.08 0.04224 0.04575 0.01733 0.999 21.11 6.9 26382
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.36 1.409 96.12 0.7331 0.794 0.3021 0.825 2.4 6.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.36 42.61 1.35 26378 3668 95.39 0.1918 0.1904 0.1904 0.2098 0.2098
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 7.777 f_angle_d 0.978 f_chiral_restr 0.084 f_plane_restr 0.013 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 954 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 37
Software Software Software Name Purpose PHENIX refinement XDS data reduction PHENIX phasing PHENIX refinement XDS data scaling