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PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z952016136
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 2.22 44.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.854 α = 90 b = 60.854 β = 90 c = 35.496 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 2023-02-10 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 1.91 30.66 99.2 0.141 0.146 0.04 0.999 10.8 13.8 10191
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 1.91 1.96 98.2 7.31 7.58 1.989 0.31 14.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 8Q53 1.91 30.68 9624 400 97.64 0.2211 0.2189 0.2756 0.2709 RANDOM 54.217
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] -0.61 -0.61 1.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.003 r_dihedral_angle_4_deg 24.616 r_dihedral_angle_3_deg 14.969 r_dihedral_angle_1_deg 6.362 r_mcangle_it 5.91 r_mcbond_it 4.465 r_mcbond_other 4.451 r_angle_refined_deg 1.549 r_angle_other_deg 1.199 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.003 r_dihedral_angle_4_deg 24.616 r_dihedral_angle_3_deg 14.969 r_dihedral_angle_1_deg 6.362 r_mcangle_it 5.91 r_mcbond_it 4.465 r_mcbond_other 4.451 r_angle_refined_deg 1.549 r_angle_other_deg 1.199 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 954 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing