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PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z1198233191
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8Q53 8Q53
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 2.23 44.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.587 α = 90 b = 60.587 β = 90 c = 35.927 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 PILATUS 6M 2023-02-08 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92124 Diamond I04-1
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 2.03 30.91 100 0.186 0.194 0.053 0.999 12.3 13.6 8621
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.03 2.08 100 11.319 3 0.363 14
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 FOURIER SYNTHESIS THROUGHOUT 8Q53 2.03 30.92 8268 330 99.9 0.1924 0.1901 0.2176 0.2485 0.2755 RANDOM 65.188
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] 0.89 0.89 -1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.458 r_dihedral_angle_4_deg 19.531 r_dihedral_angle_3_deg 16.232 r_dihedral_angle_1_deg 7.034 r_mcangle_it 6.986 r_mcbond_other 4.671 r_mcbond_it 4.653 r_angle_refined_deg 1.547 r_angle_other_deg 1.178 r_chiral_restr 0.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.458 r_dihedral_angle_4_deg 19.531 r_dihedral_angle_3_deg 16.232 r_dihedral_angle_1_deg 7.034 r_mcangle_it 6.986 r_mcbond_other 4.671 r_mcbond_it 4.653 r_angle_refined_deg 1.547 r_angle_other_deg 1.178 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 954 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing