☰ Navigation Tabs
Crystal structure of the D116N 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 4XTO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 8 293 1.2 M NaMal pH 8.0
Crystal Properties Matthews coefficient Solvent content 3.47 64.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.343 α = 90 b = 240.477 β = 90 c = 135.415 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 16M 2018-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.978 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 2.35 48.13 99.9 0.11 0.119 0.045 0.999 11.3 6.9 89161
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 2.35 2.39 99.9 1.925 2.09 0.808 0.787 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 2.35 20 84508 4459 99.73 0.1972 0.1961 0.2098 0.2175 0.2331 RANDOM 32.34
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] 4.27 -7.04 2.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.689 r_dihedral_angle_4_deg 20.388 r_dihedral_angle_3_deg 17.799 r_dihedral_angle_1_deg 6.586 r_angle_other_deg 2.375 r_angle_refined_deg 1.088 r_chiral_restr 0.043 r_bond_other_d 0.034 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.689 r_dihedral_angle_4_deg 20.388 r_dihedral_angle_3_deg 17.799 r_dihedral_angle_1_deg 6.586 r_angle_other_deg 2.375 r_angle_refined_deg 1.088 r_chiral_restr 0.043 r_bond_other_d 0.034 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10737 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 445
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing