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Crystal structure of the steady-state-SMX activated state of the light-driven sodium pump KR2 in the pentameric form at room temperature, pH 8.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XYT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 8 293 1.2 M NaMal pH 8.0
Crystal Properties Matthews coefficient Solvent content 3.65 66.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.21 α = 90 b = 240.34 β = 90 c = 138.37 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 293 PIXEL DECTRIS PILATUS3 S 6M 2019-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) R Split (All) 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 2.5 69.19 100 0.988 0.152 11.3 894.5 77967
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 100 0.488 1.5 0.72 640.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6xyt 2.7 50.01 58999 3067 99.96 0.193 0.1916 0.2003 0.2201 0.2281 RANDOM 60.461
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] 5.95 -9.07 3.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.264 r_dihedral_angle_3_deg 8.98 r_dihedral_angle_4_deg 5.865 r_dihedral_angle_1_deg 2.111 r_angle_refined_deg 1.075 r_angle_other_deg 1.041 r_chiral_restr 0.037 r_gen_planes_refined 0.002 r_bond_refined_d 0.001 r_bond_other_d
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.264 r_dihedral_angle_3_deg 8.98 r_dihedral_angle_4_deg 5.865 r_dihedral_angle_1_deg 2.111 r_angle_refined_deg 1.075 r_angle_other_deg 1.041 r_chiral_restr 0.037 r_gen_planes_refined 0.002 r_bond_refined_d 0.001 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10769 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 741
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction CrystFEL data reduction MOLREP phasing