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Crystal structure of the light-driven sodium pump KR2 in the pentameric "dry" form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XTO
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 3.27 62.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.184 α = 90 b = 239.719 β = 90 c = 131.909 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 ID30B 0.976 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 3 47.28 99.9 0.304 0.33 0.127 0.989 5.7 6.6 41018
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 3 3.12 100 1.475 1.601 0.618 0.662 6.6
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 4XTO 3 47.32 38937 2059 99.92 0.2184 0.2166 0.2276 0.2519 0.2604 RANDOM 43.925
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] 5.3 -6.49 1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.261 r_dihedral_angle_4_deg 26.713 r_dihedral_angle_3_deg 19.243 r_dihedral_angle_1_deg 7.637 r_angle_other_deg 0.766 r_angle_refined_deg 0.59 r_chiral_restr 0.028 r_bond_refined_d 0.003 r_gen_planes_refined 0.002 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.261 r_dihedral_angle_4_deg 26.713 r_dihedral_angle_3_deg 19.243 r_dihedral_angle_1_deg 7.637 r_angle_other_deg 0.766 r_angle_refined_deg 0.59 r_chiral_restr 0.028 r_bond_refined_d 0.003 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10841 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 206
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing