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Crystal structure of the light-driven sodium pump ErNaR in the monomeric form at pH 8.8
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 8.8 293 0.1M sodium acetate, 10% PEG550MME,
soaked in 0.1M Tris-HCl pH 8.8, 10% PEG550MME prior to crystal harvesting.
Crystal Properties Matthews coefficient Solvent content 2.34 47.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.382 α = 90 b = 53.382 β = 90 c = 364.842 γ = 120
Symmetry Space Group P 61 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 EIGER X 16M 2022-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.976 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.707 46.23 94.66 0.038 0.9991 13.769 37.6 26414
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.707 1.875 0.518 0.7444 1.59
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.71 20 25066 1304 75.49 0.18443 0.18271 0.1944 0.21819 0.2251 RANDOM 29.838
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] 0.27 0.14 0.27 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.68 r_dihedral_angle_3_deg 13.515 r_dihedral_angle_4_deg 13.013 r_long_range_B_other 6.728 r_long_range_B_refined 6.722 r_scangle_other 5.449 r_dihedral_angle_1_deg 5.135 r_mcangle_other 3.808 r_mcangle_it 3.804 r_scbond_other 3.681
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.68 r_dihedral_angle_3_deg 13.515 r_dihedral_angle_4_deg 13.013 r_long_range_B_other 6.728 r_long_range_B_refined 6.722 r_scangle_other 5.449 r_dihedral_angle_1_deg 5.135 r_mcangle_other 3.808 r_mcangle_it 3.804 r_scbond_other 3.681 r_scbond_it 3.676 r_mcbond_it 2.828 r_mcbond_other 2.812 r_angle_other_deg 1.113 r_angle_refined_deg 1.046 r_chiral_restr 0.049 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_gen_planes_other 0.001 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2168 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 214
Software Software Software Name Purpose REFMAC refinement MOLREP phasing XDS data reduction STARANISO data scaling