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Crystal structure of the light-driven sodium pump KR2 in the pentameric form, pH 5.0
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 3.42 64.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.241 α = 90 b = 241.392 β = 90 c = 135.109 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 2018-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.978 ESRF ID30B
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 2.6 48.08 98.9 0.087 0.096 0.041 0.999 9.7 5.5 64789
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 2.6 2.66 99.8 1.746 1.924 0.794 0.448 5.7
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 2.6 48.13 61464 3301 98.62 0.1928 0.191 0.1999 0.2247 0.2274 RANDOM 72.949
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] 5.87 -5.76 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.16 r_dihedral_angle_4_deg 20.643 r_dihedral_angle_3_deg 17.428 r_dihedral_angle_1_deg 7.456 r_angle_other_deg 0.761 r_angle_refined_deg 0.542 r_chiral_restr 0.031 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.16 r_dihedral_angle_4_deg 20.643 r_dihedral_angle_3_deg 17.428 r_dihedral_angle_1_deg 7.456 r_angle_other_deg 0.761 r_angle_refined_deg 0.542 r_chiral_restr 0.031 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10900 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 422
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing