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Crystal structure of GABARAP in complex with KBTBD6 LIR peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D32
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.2 M Ammonium acetate, 0.01 M Magnesium acetate tetrahydrate, 30% Poly ethylene glycol 8000, 0.1 M Tris-HCl, pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.19 43.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.893 α = 65.3 b = 57.353 β = 77.34 c = 67.31 γ = 89.95
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 PIXEL PSI PILATUS 6M 2014-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 37.75 92.7 0.043 12.1 2.5 37496
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 91 0.365 2.5 2.4 5380
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 MOLECULAR REPLACEMENT THROUGHOUT 3D32 1.9 32.73 35614 1881 92.65 0.2013 0.1982 0.2049 0.2582 0.2604 RANDOM 33.186
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] 5.04 0.47 0.75 -1.19 0.96 -2.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.437 r_dihedral_angle_3_deg 17.586 r_dihedral_angle_4_deg 15.396 r_dihedral_angle_1_deg 7.857 r_angle_refined_deg 1.162 r_angle_other_deg 0.635 r_chiral_restr 0.079 r_gen_planes_refined 0.014 r_bond_refined_d 0.009 r_gen_planes_other 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.437 r_dihedral_angle_3_deg 17.586 r_dihedral_angle_4_deg 15.396 r_dihedral_angle_1_deg 7.857 r_angle_refined_deg 1.162 r_angle_other_deg 0.635 r_chiral_restr 0.079 r_gen_planes_refined 0.014 r_bond_refined_d 0.009 r_gen_planes_other 0.001 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4254 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling MOLREP phasing