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Crystal structure of the light-driven inward proton pump xenorhodopsin BcXeR in the M state at pH 5.2 in the presence of sodium at 100K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XIO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 293 0.8 M Na/K-Pi pH 8.2
crystals soaked in 1.2 M Na/K-Pi pH 5.2 before harvesting
Crystal Properties Matthews coefficient Solvent content 2.89 57.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.5 α = 90 b = 109.5 β = 90 c = 119 γ = 90
Symmetry Space Group P 21 21 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 2021-03-25 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) R Merge I (Observed) 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 1.9 49.738 95.3 0.078 0.999 17.5 13.1 62940
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.963 1.948 0.554 1.5
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 1xio 1.9 20 59830 3046 88.25 0.1981 0.1966 0.2083 0.2276 0.2376 RANDOM 33.732
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] 1.07 0.19 -1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.655 r_dihedral_angle_4_deg 17.984 r_dihedral_angle_3_deg 13.906 r_dihedral_angle_1_deg 4.599 r_angle_other_deg 1.045 r_angle_refined_deg 1.022 r_chiral_restr 0.049 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.655 r_dihedral_angle_4_deg 17.984 r_dihedral_angle_3_deg 13.906 r_dihedral_angle_1_deg 4.599 r_angle_other_deg 1.045 r_angle_refined_deg 1.022 r_chiral_restr 0.049 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5245 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 637
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing