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Crystal structure of TolB from Acinetobacter baumannii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2W8B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 1.1 M sodium/potassium tartrate, 0.1 M Tris pH 8.5, 2% (w/v) PEG 400
Crystal Properties Matthews coefficient Solvent content 2.05 39.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.498 α = 90 b = 98.443 β = 92.072 c = 83.832 γ = 90
Symmetry Space Group P 1 21 1
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 IV 2020-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.42 30 98.8 0.085 0.052 10.63 3.5 26751 39.06
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.42 2.46 84.7 0.458 0.349 0.708 1.09 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2W8B 2.42 29.63 1.38 26729 1343 98.67 0.1963 0.1937 0.1934 0.2437 0.2434 51.09
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.6856 f_angle_d 0.6666 f_chiral_restr 0.0607 f_plane_restr 0.0049 f_bond_d 0.0025
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6174 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling BALBES phasing ARP/wARP model building PHENIX model building Coot model building