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Crystal structure of the steady-state 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 3.64 66.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.189 α = 90 b = 239.861 β = 90 c = 138.456 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 EIGER X 16M 2019-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.976 PETRA III, EMBL c/o DESY P14 (MX2)
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 2.59 48.81 99.6 0.237 0.252 0.086 0.994 6.7 8.5 69594
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.59 2.65 94.8 2.131 2.27 0.771 0.507 8.6
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 2.6 20 65587 3487 99.63 0.1861 0.1847 0.1967 0.2123 0.2187 RANDOM 49.282
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] 4.56 -6.08 1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.042 r_dihedral_angle_3_deg 9.089 r_dihedral_angle_4_deg 6.007 r_dihedral_angle_1_deg 2.18 r_angle_refined_deg 1.077 r_angle_other_deg 1.045 r_chiral_restr 0.038 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 23.042 r_dihedral_angle_3_deg 9.089 r_dihedral_angle_4_deg 6.007 r_dihedral_angle_1_deg 2.18 r_angle_refined_deg 1.077 r_angle_other_deg 1.045 r_chiral_restr 0.038 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 Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing