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Crystal structure of Optineurin LIR-fused human LC3B_2-119
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VTU PDB ENTRY 3VTU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 289 2.0M Ammonium sulfate, 0.05M Tri-sodium citrate, 0.1M Potassium sodium tartrate, 10% PEG 3350, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.82 32.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.2 α = 90 b = 53 β = 90 c = 60.96 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX225HE 2011-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
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 1.58 29.32 100 0.261 5.7 16222
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 1.58 1.67 100 0.632 3.5 2324
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 PDB ENTRY 3VTU 1.7 29.32 12438 640 99.97 0.19426 0.19158 0.1914 0.25168 0.2491 RANDOM 17.036
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] 0.08 0.34 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.099 r_dihedral_angle_4_deg 21.682 r_dihedral_angle_3_deg 13.727 r_dihedral_angle_1_deg 6.569 r_scangle_it 5.918 r_scbond_it 3.757 r_mcangle_it 2.559 r_angle_refined_deg 2.161 r_mcbond_it 1.502 r_chiral_restr 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.099 r_dihedral_angle_4_deg 21.682 r_dihedral_angle_3_deg 13.727 r_dihedral_angle_1_deg 6.569 r_scangle_it 5.918 r_scbond_it 3.757 r_mcangle_it 2.559 r_angle_refined_deg 2.161 r_mcbond_it 1.502 r_chiral_restr 0.15 r_bond_refined_d 0.025 r_gen_planes_refined 0.014 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1034 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 5
Software Software Software Name Purpose MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling