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PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z1688504114
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 2.24 44.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.917 α = 90 b = 60.917 β = 90 c = 35.653 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 1.92 43.08 99.8 0.113 0.118 0.032 0.999 11.6 13.6 10230
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 1.92 1.96 97.5 3.518 3.652 0.975 0.268 14.1
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 1.92 43.11 9804 407 99.75 0.1994 0.1973 0.2169 0.2506 0.2677 RANDOM 50.216
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] -0.52 -0.52 1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.927 r_dihedral_angle_4_deg 21.757 r_dihedral_angle_3_deg 15.886 r_dihedral_angle_1_deg 6.453 r_mcangle_it 5.103 r_mcbond_it 3.446 r_mcbond_other 3.445 r_angle_refined_deg 1.594 r_angle_other_deg 1.206 r_chiral_restr 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.927 r_dihedral_angle_4_deg 21.757 r_dihedral_angle_3_deg 15.886 r_dihedral_angle_1_deg 6.453 r_mcangle_it 5.103 r_mcbond_it 3.446 r_mcbond_other 3.445 r_angle_refined_deg 1.594 r_angle_other_deg 1.206 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 954 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing