☰ Navigation Tabs
Crystal structure of the light-driven inward proton pump xenorhodopsin BcXeR in the ground state at pH 8.2 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
Crystal Properties Matthews coefficient Solvent content 2.89 57.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.24 α = 90 b = 109.57 β = 90 c = 119.47 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 EIGER2 X 16M 2021-12-20 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 1.7 49.799 93.12 0.079 0.993 15.9 13.8 91083
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 1.7 1.742 78.8 3.353 0.352 0.9
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 1.7 20 86518 4504 91.86 0.176 0.1745 0.1888 0.2034 0.2157 RANDOM 33.56
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] 0.52 0.3 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.251 r_dihedral_angle_4_deg 19.404 r_dihedral_angle_3_deg 12.296 r_dihedral_angle_1_deg 4.924 r_angle_other_deg 1.238 r_angle_refined_deg 1.223 r_chiral_restr 0.075 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.251 r_dihedral_angle_4_deg 19.404 r_dihedral_angle_3_deg 12.296 r_dihedral_angle_1_deg 4.924 r_angle_other_deg 1.238 r_angle_refined_deg 1.223 r_chiral_restr 0.075 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5262 Nucleic Acid Atoms Solvent Atoms 283 Heterogen Atoms 750
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing