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Crystal structure of human Gamma-Aminobutyric Acid Receptor-Associated Protein-like 1 (GABARAP1), Isoform CRA_a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GNU PDB entry 1GNU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 291 25% PEG 3350, 0.2M Sodium chloride, 0.1M Hepes, 5% MPD, pH 7.5, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.1 41.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.86 α = 111.09 b = 38.193 β = 95.91 c = 45.746 γ = 108.05
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS 2007-08-10 M SINGLE WAVELENGTH 2 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS 2007-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ DW 1.5418 2 ROTATING ANODE RIGAKU FR-E+ DW 1.5418
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 1,2 1.65 30 94.9 0.042 27.5 3.5 24587
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) 1.65 1.71 65 0.082 2.2 1689
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 (All) 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 PDB entry 1GNU 1.65 18.5 24551 910 95.045 0.201 0.201 0.2 0.2057 0.234 0.2327 thin shells 16.9
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] 0.432 -0.07 -1.123 -0.474 -0.43 -0.542
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.967 r_dihedral_angle_4_deg 18.266 r_dihedral_angle_3_deg 13.147 r_dihedral_angle_1_deg 6.018 r_scangle_it 3.805 r_mcangle_it 3.482 r_scbond_it 2.81 r_mcbond_it 2.689 r_angle_refined_deg 1.449 r_angle_other_deg 0.902
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.967 r_dihedral_angle_4_deg 18.266 r_dihedral_angle_3_deg 13.147 r_dihedral_angle_1_deg 6.018 r_scangle_it 3.805 r_mcangle_it 3.482 r_scbond_it 2.81 r_mcbond_it 2.689 r_angle_refined_deg 1.449 r_angle_other_deg 0.902 r_mcbond_other 0.787 r_symmetry_vdw_other 0.283 r_nbd_refined 0.213 r_nbd_other 0.195 r_nbtor_refined 0.186 r_symmetry_hbond_refined 0.134 r_xyhbond_nbd_refined 0.121 r_chiral_restr 0.093 r_nbtor_other 0.082 r_symmetry_vdw_refined 0.079 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1905 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 3
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction