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X-ray structure of the Legionella pneumophila ATPase DotB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EWV 2EWV, 5FL3 experimental model PDB 5FL3 2EWV, 5FL3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 1.2M of Na/K phosphate buffer pH 7.2
Crystal Properties Matthews coefficient Solvent content 2.5 50.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.2 α = 83.7 b = 109.3 β = 86.6 c = 119.8 γ = 60.7
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2017-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976250 Diamond I03
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 3.19 36.04 98 6.95 3.49 78104
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.19 3.31
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 2EWV, 5FL3 3.19 36.04 78095 3841 97.99 0.2345 0.2331 0.2345 0.2613 0.2601 RANDOM 100.4151
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] -0.11 0.5 0.36 -0.63 -0.42 1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.303 r_dihedral_angle_4_deg 19.676 r_dihedral_angle_3_deg 19.383 r_dihedral_angle_1_deg 6.911 r_mcangle_it 6.179 r_mcbond_it 3.788 r_mcbond_other 3.788 r_angle_other_deg 3.578 r_angle_refined_deg 1.536 r_chiral_restr 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.303 r_dihedral_angle_4_deg 19.676 r_dihedral_angle_3_deg 19.383 r_dihedral_angle_1_deg 6.911 r_mcangle_it 6.179 r_mcbond_it 3.788 r_mcbond_other 3.788 r_angle_other_deg 3.578 r_angle_refined_deg 1.536 r_chiral_restr 0.1 r_bond_refined_d 0.016 r_gen_planes_other 0.011 r_gen_planes_refined 0.009 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 34602 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing