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Crystal structure of the light-driven sodium pump KR2 in the pentameric "wet" form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XTN 4XTN chain D
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 3.43 64.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.628 α = 90 b = 240.474 β = 90 c = 135.614 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 EIGER X 4M 2017-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.976 ESRF MASSIF-3
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 2.8 48.13 99.6 0.141 0.16 0.072 0.997 5.6 4.5 52539
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 2.8 2.89 99.4 1.29 1.448 0.645 0.782 4.7
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 4XTN chain D 2.8 48.17 49912 2623 99.4 0.19 0.1883 0.1991 0.2233 0.2324 RANDOM 61.866
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] 9.7 -8.1 -1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.856 r_dihedral_angle_4_deg 21.151 r_dihedral_angle_3_deg 16.55 r_dihedral_angle_1_deg 7.844 r_angle_other_deg 0.724 r_angle_refined_deg 0.6 r_chiral_restr 0.028 r_bond_refined_d 0.003 r_gen_planes_refined 0.002 r_bond_other_d
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.856 r_dihedral_angle_4_deg 21.151 r_dihedral_angle_3_deg 16.55 r_dihedral_angle_1_deg 7.844 r_angle_other_deg 0.724 r_angle_refined_deg 0.6 r_chiral_restr 0.028 r_bond_refined_d 0.003 r_gen_planes_refined 0.002 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10942 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 900
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing