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Crystal structure of the D116N mutant of the light-driven sodium pump KR2 in the monomeric form, pH 4.6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XTL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 4.6 293 2 M NaMal pH 4.6
Crystal Properties Matthews coefficient Solvent content 3.23 61.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.887 α = 90 b = 83.601 β = 90 c = 233.83 γ = 90
Symmetry Space Group I 2 2 2
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 S 6M 2018-08-26 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 1.8 40.81 99.8 0.046 0.05 0.02 0.999 16.2 6.6 37771
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 1.8 1.84 99.7 1 1.081 0.406 0.905 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 4xtl 1.8 19.83 35822 1921 99.65 0.2023 0.2013 0.2121 0.22 0.2276 RANDOM 43.739
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] 0.25 0.41 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.118 r_dihedral_angle_4_deg 27.804 r_dihedral_angle_3_deg 12.954 r_dihedral_angle_1_deg 4.729 r_angle_other_deg 1.097 r_angle_refined_deg 1.068 r_chiral_restr 0.053 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.118 r_dihedral_angle_4_deg 27.804 r_dihedral_angle_3_deg 12.954 r_dihedral_angle_1_deg 4.729 r_angle_other_deg 1.097 r_angle_refined_deg 1.068 r_chiral_restr 0.053 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2147 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 269
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing