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Structure of dimeric sodium proton antiporter NhaA, at pH 8.5, crystallized with chimeric Fab antibodies
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZCD 1zcd, 2yk1 experimental model PDB 2YK1 1zcd, 2yk1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 292 100 mM Tris pH 8.5, 100 mM MgCl2, 100 mM NaCl, 32 % PEG400
Crystal Properties Matthews coefficient Solvent content 4.2 66.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.788 α = 90 b = 92.163 β = 109.885 c = 139.105 γ = 90
Symmetry Space Group P 1 21 1
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 2018-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.979 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.04 24.86 94.1 0.087 0.999 16 13.1 94893 52.71
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.34 67.6 1.68 0.428 1.8 11.1
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 FREE R-VALUE 1zcd, 2yk1 2.04 24.86 1.35 94883 2414 56.06 0.1991 0.1982 0.1997 0.2347 0.2354 78.38
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.4573 f_angle_d 0.6549 f_chiral_restr 0.0449 f_plane_restr 0.0045 f_bond_d 0.0038
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11858 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 185
Software Software Software Name Purpose MxCuBE data collection PHENIX refinement STARANISO data scaling XDS data reduction PHASER phasing Coot model building