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Crystal structure of T7-tagged 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, 5% Glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.85 56.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.17 α = 90 b = 64.12 β = 90 c = 149.77 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 ADSC QUANTUM 210r 2011-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 2.52 49.92 97.5 0.128 12.9 20055
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 2.52 2.66 95.9 0.701 3 2828
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 2.52 49.92 18984 1025 97.15 0.21479 0.21127 0.2086 0.27953 0.2724 RANDOM 36.628
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] -0.31 -2.71 3.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.435 r_dihedral_angle_4_deg 21.844 r_dihedral_angle_3_deg 20.753 r_dihedral_angle_1_deg 7.186 r_scangle_it 4.51 r_scbond_it 2.629 r_angle_refined_deg 1.9 r_mcangle_it 1.843 r_mcbond_it 0.965 r_chiral_restr 0.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.435 r_dihedral_angle_4_deg 21.844 r_dihedral_angle_3_deg 20.753 r_dihedral_angle_1_deg 7.186 r_scangle_it 4.51 r_scbond_it 2.629 r_angle_refined_deg 1.9 r_mcangle_it 1.843 r_mcbond_it 0.965 r_chiral_restr 0.129 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 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 3102 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 20
Software Software Software Name Purpose MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling