☰ Navigation Tabs
X-ray structure of the Deinococcus radiodurans Nramp/MntH divalent transition metal transporter WT in an inward-open, cadmium-bound 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 6.1 298 24% PEG400, 0.1 M MES, pH 6.1, 50 mM succinic acid, pH 6.0, 20 mM spermidine, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.35 47.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.137 α = 90 b = 71.369 β = 90 c = 99.054 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 PILATUS 6M-F 2018-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 1 APS 24-ID-C
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 2.48 45.54 99.4 0.164 0.184 0.083 0.996 8.1 4.9 15312 49.52
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 2.48 2.58 99.7 1.626 1.831 0.823 0.367 4.8
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 8E5S 2.48 45.54 1.33 15291 2786 97.3 0.2077 0.2029 0.2504 0.24 64.8177
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 2905 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 362
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing Coot model building