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Time-resolved structure of K+-dependent Na+-PPase from Thermotoga maritima 300-seconds post reaction initiation with Na+
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8B21 D_1292125586
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 60 mM Tris-HCl pH 8.0, 26% v/v PEG400, 175 mM KCl, 2.4 mM MgCl2, 2 mM K4PPi, 20 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.99 58.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.928 α = 90 b = 110.626 β = 108.26 c = 106.154 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 EIGER2 X 16M 2019-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9762 PETRA III, EMBL c/o DESY P14 (MX2)
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.97 100.81 95.7 0.975 6.1 6.4 14163 88.03
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.97 4.09 0.837
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 D_1292125586 3.98 79.7 1.36 14119 1400 88.16 0.2357 0.2326 0.2327 0.2653 0.2645 132.51
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 10.2414 f_angle_d 0.5903 f_chiral_restr 0.0396 f_plane_restr 0.0043 f_bond_d 0.0032
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10431 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 13
Software Software Software Name Purpose PHENIX refinement XDS data reduction STARANISO data scaling PHASER phasing