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Crystal structure of the potassium-pumping G263F mutant of the light-driven sodium pump KR2 in the pentameric form, pH 8.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6REW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 293 3.4 M Sodium Malonate pH 8.0
Crystal Properties Matthews coefficient Solvent content 3.41 63.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.68 α = 90 b = 239.685 β = 90 c = 134.584 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 100 PIXEL DECTRIS PILATUS3 6M 2018-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.003 ESRF ID29
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 2.4 47.97 100 0.131 0.142 0.055 0.998 10.3 6.7 83371
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 2.4 2.45 100 2.283 2.467 0.928 0.425 7
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 6REW 2.4 47.97 78915 4195 99.91 0.1741 0.1725 0.1838 0.2046 0.2103 RANDOM 54.155
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] 3.71 -5.51 1.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.772 r_dihedral_angle_4_deg 22.149 r_dihedral_angle_3_deg 16.218 r_dihedral_angle_1_deg 7.398 r_angle_other_deg 0.751 r_angle_refined_deg 0.704 r_chiral_restr 0.04 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.772 r_dihedral_angle_4_deg 22.149 r_dihedral_angle_3_deg 16.218 r_dihedral_angle_1_deg 7.398 r_angle_other_deg 0.751 r_angle_refined_deg 0.704 r_chiral_restr 0.04 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10977 Nucleic Acid Atoms Solvent Atoms 462 Heterogen Atoms 1653
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing