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Crystal structure of the light-driven inward proton pump xenorhodopsin BcXeR in the ground 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 2.91 57.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.57 α = 90 b = 109.59 β = 90 c = 119.62 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 1.8 49.817 94.9 0.104 0.999 14.1 13.1 65268
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 1.8 1.916 3.376 0.316 0.8
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 1.8 20 62007 3194 77.49 0.1982 0.1966 0.2068 0.2303 0.2394 RANDOM 32.347
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] 0.73 0.09 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.877 r_dihedral_angle_4_deg 21.82 r_dihedral_angle_3_deg 12.547 r_dihedral_angle_1_deg 4.86 r_angle_refined_deg 1.131 r_angle_other_deg 1.114 r_chiral_restr 0.064 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.877 r_dihedral_angle_4_deg 21.82 r_dihedral_angle_3_deg 12.547 r_dihedral_angle_1_deg 4.86 r_angle_refined_deg 1.131 r_angle_other_deg 1.114 r_chiral_restr 0.064 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5257 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 733
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing