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Structure of K+-dependent Na+-PPase from Thermotoga maritima in complex with zoledronate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LZQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.1 M MES pH 6.5, 0.1 M NaCl, 33 % PEG400, and 4 % ethylene glycol
Crystal Properties Matthews coefficient Solvent content 3.01 59.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.185 α = 90 b = 147.362 β = 90 c = 252.335 γ = 90
Symmetry Space Group P 21 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 2019-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.97625 Diamond I04-1
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 3.257 127.255 93.4 0.137 0.143 0.039 0.999 10.2 13.4 33220 118.02
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 3.26 3.31 1.785 0.516 0.573 1.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.26 48.22 1.34 33042 1669 55.24 0.2676 0.2655 0.265 0.3062 0.3046 109.65
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 11.8943 f_angle_d 0.6566 f_chiral_restr 0.0493 f_bond_d 0.0041 f_plane_restr 0.0035
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20730 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 115
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing