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NaK S-DI mutant soaked in Na+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E86
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 200 mM KCl, 100 mM HEPES (KOH) pH 7.5, 62% MPD (2-Methyl-2,4-pentanediol racemate) - soaked in 100 mM NaCl, 100 mM Tris-HCl pH 8.0, 50% MPD
Crystal Properties Matthews coefficient Solvent content 2.05 39.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.204 α = 90 b = 88.173 β = 90 c = 49.389 γ = 90
Symmetry Space Group C 2 2 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 2019-08-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033 PETRA III, DESY P11
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 1.7 59.73 99.8 0.06674 0.09439 0.06674 0.996 4.46 2 19895 21.96
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.761 99.69 0.9783 0.9783 0.596 0.6 2
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 3E86 1.7 59.73 1.34 19862 1969 99.8 0.1904 0.1858 0.1861 0.233 0.2335 31.23
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 13.0903 f_angle_d 0.7083 f_chiral_restr 0.0504 f_bond_d 0.0094 f_plane_restr 0.0054
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1452 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 152
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing