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Hexameric Ring Complex of Engineered V1-ATPase bound to 4 ADPs: A3(De)3_(ADP)3cat,1non-cat, Hexameric Ring Complex of Engineered V1-ATPase bound to 5 ADPs: A3(De)3_(ADP)3cat,2non-cat
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8IGU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M Tris-HCl (pH 8.5), 20% PEG 3350, 0.2M Ammonium Acetate
Crystal Properties Matthews coefficient Solvent content 2.88 57.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 179.407 α = 90 b = 125.077 β = 93.826 c = 180.914 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 EIGER X 4M 2018-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.1 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 4.2 48.92 99.9 0.24 0.095 0.994 7.2 7.5 58670 116.21
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 4.2 4.32 1.07 0.423 0.764 2.1
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 4.2 48.92 1.34 58615 2921 99.93 0.2439 0.242 0.2423 0.2811 0.2787 153.47
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 18.2336 f_angle_d 0.6513 f_chiral_restr 0.0464 f_plane_restr 0.0042 f_bond_d 0.0028
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 47540 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 252
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing