☰ Navigation Tabs
X-ray structure of the Yersinia pseudotuberculosis 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 0.1M Na/Cacodylate buffer pH5.5 and 12% PEG 8000
Crystal Properties Matthews coefficient Solvent content 3 59.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.04 α = 103.9 b = 93.56 β = 101.98 c = 109.92 γ = 99.94
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 2016-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.97626 Diamond I24
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 2.75 40.57 97.8 10.33 3.49 77292
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 2.75 2.85
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 2.75 40.56 77292 3866 97.81 0.2567 0.2546 0.2528 0.2962 0.2903 RANDOM 76.0573
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] 1.34 -0.19 0.4 -1.39 2.57 -1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.974 r_dihedral_angle_4_deg 24.385 r_dihedral_angle_3_deg 20.779 r_dihedral_angle_1_deg 9.257 r_mcangle_it 4.633 r_angle_other_deg 3.622 r_mcbond_it 2.941 r_mcbond_other 2.941 r_angle_refined_deg 1.151 r_chiral_restr 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.974 r_dihedral_angle_4_deg 24.385 r_dihedral_angle_3_deg 20.779 r_dihedral_angle_1_deg 9.257 r_mcangle_it 4.633 r_angle_other_deg 3.622 r_mcbond_it 2.941 r_mcbond_other 2.941 r_angle_refined_deg 1.151 r_chiral_restr 0.071 r_bond_refined_d 0.013 r_gen_planes_other 0.008 r_gen_planes_refined 0.006 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18021 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing