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Acinetobacter sp. Tol 5 AtaA YDD-DALL3 domains in C-terminal stalk fused to GCN4 adaptors (CstalkC1iii)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YO2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.67% PEG 2000 MME, 67mM HEPES, 667mM Succinic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.35 63.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.46 α = 90 b = 43.46 β = 90 c = 825.36 γ = 120
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 VII 2013-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.95 19.64 99.5 23200 23200
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.07 98.8 0.469 0.499 4.04
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2YO2 1.952 19.64 23198 23198 1160 99.57 0.1806 0.1806 0.1793 0.1903 0.2053 0.2108 RANDOM 35.524
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] 0.21 0.21 0.21 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.77 r_sphericity_free 29.456 r_sphericity_bonded 18.99 r_dihedral_angle_3_deg 15.366 r_dihedral_angle_1_deg 5.352 r_mcangle_it 5.242 r_mcbond_it 4.338 r_mcbond_other 4.338 r_rigid_bond_restr 3.809 r_dihedral_angle_4_deg 2.423
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.77 r_sphericity_free 29.456 r_sphericity_bonded 18.99 r_dihedral_angle_3_deg 15.366 r_dihedral_angle_1_deg 5.352 r_mcangle_it 5.242 r_mcbond_it 4.338 r_mcbond_other 4.338 r_rigid_bond_restr 3.809 r_dihedral_angle_4_deg 2.423 r_angle_refined_deg 1.38 r_angle_other_deg 0.82 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 786 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 1
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection XDS data reduction XDS data scaling MOLREP phasing