☰ Navigation Tabs
X-ray structure of the Deinococcus radiodurans Nramp/MntH divalent transition metal transporter WTsoak in an occluded state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8E5S PDB entry 8E5S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 6.3 298 28% PEG400, 0.1 M MES, pH 6.3, 50 mM succinic acid, pH 6.0, 5 mM spermidine, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.32 47.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.954 α = 90 b = 71.037 β = 90 c = 98.773 γ = 90
Symmetry Space Group P 2 21 21
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 EIGER X 16M 2021-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.36 41.23 99.2 0.107 0.128 0.069 0.997 5.8 3.3 17464 49.97
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.36 2.45 99.5 1.328 1.581 0.846 0.389 3.4
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 THROUGHOUT PDB entry 8E5S 2.36 41.23 1.34 17432 1743 98.74 0.2198 0.2169 0.2172 0.2458 0.2456 65.1889
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2923 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 443
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing Coot model building