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Crystal structure of the light-driven sodium pump ErNaR in the monomeric form at 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 0.1M sodium acetate pH 4.6, 10% PEG 550MME.
Crystal Properties Matthews coefficient Solvent content 2.35 47.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.401 α = 90 b = 53.401 β = 90 c = 365.052 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 2021-03-29 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 1.664 60.842 94.2 0.052 0.9987 11.038 35.9 30115
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 1.664 1.763 78.4 1.161 0.3574 0.698
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.7 20 28309 1468 83.4 0.21354 0.21178 0.24781 0.2307 RANDOM 29.044
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] 0.26 0.13 0.26 -0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.926 r_dihedral_angle_4_deg 14.674 r_dihedral_angle_3_deg 13.87 r_long_range_B_other 6.41 r_long_range_B_refined 6.407 r_scangle_other 5.124 r_dihedral_angle_1_deg 5.042 r_scbond_other 3.573 r_scbond_it 3.572 r_mcangle_it 3.571
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.926 r_dihedral_angle_4_deg 14.674 r_dihedral_angle_3_deg 13.87 r_long_range_B_other 6.41 r_long_range_B_refined 6.407 r_scangle_other 5.124 r_dihedral_angle_1_deg 5.042 r_scbond_other 3.573 r_scbond_it 3.572 r_mcangle_it 3.571 r_mcangle_other 3.571 r_mcbond_it 2.748 r_mcbond_other 2.742 r_angle_other_deg 1.138 r_angle_refined_deg 1.025 r_chiral_restr 0.046 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d r_gen_planes_other 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 87 Heterogen Atoms 147
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling MOLREP phasing