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1.42 Angstrom Resolution Crystal Structure of Translocation Protein TolB from Salmonella enterica
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 7.5 295 Protein: 5.2 mg/ml, 0.01M Tris HCl (pH 8.3);
Screen: PACT (G4), 0.2 M Potassium thiocyanate, 0.1 M Bis Tris propane pH 7.5, 20% (w/v) PEG 3350.
Crystal Properties Matthews coefficient Solvent content 2.14 42.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.894 α = 90 b = 40.57 β = 111.61 c = 77.994 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 CCD MARMOSAIC 300 mm CCD C(111) 2019-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) 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 1.42 30 96.2 0.054 0.054 0.062 0.029 22.8 4.2 67628 -3 13.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.42 1.44 100 0.622 0.622 0.726 0.368 0.709 2.1 3.8
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 2w8b 1.42 29.7 64124 3474 95.83 0.1635 0.1618 0.1713 0.1944 0.2038 RANDOM 16.254
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] 1.22 -0.7 -0.29 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.75 r_dihedral_angle_4_deg 10.771 r_dihedral_angle_3_deg 9.774 r_dihedral_angle_1_deg 4.512 r_angle_refined_deg 1.423 r_rigid_bond_restr 0.983 r_angle_other_deg 0.409 r_chiral_restr 0.065 r_gen_planes_refined 0.053 r_gen_planes_other 0.049
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.75 r_dihedral_angle_4_deg 10.771 r_dihedral_angle_3_deg 9.774 r_dihedral_angle_1_deg 4.512 r_angle_refined_deg 1.423 r_rigid_bond_restr 0.983 r_angle_other_deg 0.409 r_chiral_restr 0.065 r_gen_planes_refined 0.053 r_gen_planes_other 0.049 r_bond_refined_d 0.006 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3101 Nucleic Acid Atoms Solvent Atoms 477 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing