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PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z56767614
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 45.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.091 α = 90 b = 61.091 β = 90 c = 35.54 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 2.09 43.19 99.9 0.124 0.129 0.035 0.997 10.4 13.5 7949
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 2.09 2.15 99.3 3.388 3.517 0.937 0.378 13.8
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 2.09 43.24 7594 299 99.38 0.1917 0.1891 0.2112 0.2559 0.2844 RANDOM 59.148
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] 0.16 0.16 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.335 r_dihedral_angle_4_deg 21.92 r_dihedral_angle_3_deg 16.102 r_dihedral_angle_1_deg 6.486 r_mcangle_it 6.155 r_mcbond_it 4.123 r_mcbond_other 4.119 r_angle_refined_deg 1.482 r_angle_other_deg 1.181 r_chiral_restr 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.335 r_dihedral_angle_4_deg 21.92 r_dihedral_angle_3_deg 16.102 r_dihedral_angle_1_deg 6.486 r_mcangle_it 6.155 r_mcbond_it 4.123 r_mcbond_other 4.119 r_angle_refined_deg 1.482 r_angle_other_deg 1.181 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 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 50
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing