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X-ray structure of the Deinococcus radiodurans Nramp/MntH divalent transition metal transporter A47W mutant in an occluded, manganese-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 7.2 298 20% PEG550 MME, 0.1 M HEPES, pH 7.2, 0.25 M sodium chloride, 10 mM manganese chloride
Crystal Properties Matthews coefficient Solvent content 2.31 42.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.98 α = 90 b = 70.929 β = 90 c = 98.571 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 2018-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.984 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 2.39 45.35 99 0.163 0.191 0.097 0.994 7.1 3.6 16773 40.33
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 2.39 2.48 99.7 1.396 1.621 0.811 0.399 3.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 8E5S 2.39 45.35 1.34 16734 1673 98.6 0.2101 0.2059 0.2063 0.2464 0.2465 50.379
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 2939 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 469
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing Coot model building