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Crystal structure of the light-driven inward proton pump xenorhodopsin BcXeR in the ground state at pH 8.2 at room temperature, 500-mks-long snapshots
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
Crystal Properties Matthews coefficient Solvent content 3.11 60.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.91 α = 90 b = 111.86 β = 90 c = 119.52 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 293 PIXEL DECTRIS EIGER2 X 16M 2021-11-25 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 Split (All) 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 2.3 45.96 100 0.192 4 526.2 45120
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 3.609
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 2.3 20 41079 2136 99.19 0.2197 0.2181 0.23 0.2509 0.274 RANDOM 49.699
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] 2.83 -0.25 -2.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.167 r_dihedral_angle_4_deg 18.554 r_dihedral_angle_3_deg 13.473 r_dihedral_angle_1_deg 4.437 r_angle_refined_deg 1.04 r_angle_other_deg 0.993 r_chiral_restr 0.038 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.167 r_dihedral_angle_4_deg 18.554 r_dihedral_angle_3_deg 13.473 r_dihedral_angle_1_deg 4.437 r_angle_refined_deg 1.04 r_angle_other_deg 0.993 r_chiral_restr 0.038 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5222 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 550
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrystFEL data reduction CrystFEL data scaling MOLREP phasing