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Crystal structure of the light-driven sodium pump KR2 in the monomeric form, pH 6.0
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 293 2.0 M Sodium Malonate pH 4.3
Crystal Properties Matthews coefficient Solvent content 3.12 60.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.334 α = 90 b = 81.246 β = 90 c = 233.359 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 6M 2016-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.000 ESRF ID23-1
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 2.3 40.62 99.7 0.105 0.116 0.049 0.997 10.4 5.4 17576
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 2.3 2.39 99.5 1.058 1.177 0.506 0.683 5.2
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 2.3 20 16711 831 99.31 0.2047 0.202 0.216 0.2585 0.2642 RANDOM 43.942
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] 4.53 0.14 -4.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.858 r_dihedral_angle_4_deg 20.175 r_dihedral_angle_3_deg 15.641 r_dihedral_angle_1_deg 7.085 r_angle_other_deg 0.725 r_angle_refined_deg 0.584 r_chiral_restr 0.034 r_bond_refined_d 0.003 r_gen_planes_refined 0.002 r_gen_planes_other 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.858 r_dihedral_angle_4_deg 20.175 r_dihedral_angle_3_deg 15.641 r_dihedral_angle_1_deg 7.085 r_angle_other_deg 0.725 r_angle_refined_deg 0.584 r_chiral_restr 0.034 r_bond_refined_d 0.003 r_gen_planes_refined 0.002 r_gen_planes_other 0.001 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2134 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 276
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing