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Crystal structure of the light-driven sodium pump KR2 in the pentameric form, pH 6.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XTN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 293 3.4 M Sodium Malonate pH 6.0
Crystal Properties Matthews coefficient Solvent content 3.46 64.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.432 α = 90 b = 240.787 β = 90 c = 135.737 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 PILATUS 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 2.7 48.21 96.9 0.19 0.212 0.091 0.991 7.9 4.8 57277
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 2.7 2.77 98.6 1.308 1.458 0.627 0.632 4.7
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 2.7 48.26 54451 2803 96.47 0.2242 0.2229 0.2318 0.2503 0.256 RANDOM 39.003
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] 3.82 -4.67 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.859 r_dihedral_angle_4_deg 22.495 r_dihedral_angle_3_deg 16.338 r_dihedral_angle_1_deg 7.608 r_angle_other_deg 0.72 r_angle_refined_deg 0.56 r_chiral_restr 0.029 r_bond_refined_d 0.002 r_bond_other_d 0.002 r_gen_planes_refined 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.859 r_dihedral_angle_4_deg 22.495 r_dihedral_angle_3_deg 16.338 r_dihedral_angle_1_deg 7.608 r_angle_other_deg 0.72 r_angle_refined_deg 0.56 r_chiral_restr 0.029 r_bond_refined_d 0.002 r_bond_other_d 0.002 r_gen_planes_refined 0.002 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10942 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 904
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing