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Crystal structure of the 48C12 heliorhodopsin in the blue form at pH 4.3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HYJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 293 The crystals were grown using in meso crystallization technique.
Precipitant: 2.4 M AmSO4; pH 4.3
Crystal Properties Matthews coefficient Solvent content 2.82 56.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.177 α = 90 b = 60.744 β = 92.02 c = 92.913 γ = 90
Symmetry Space Group P 1 21 1
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 9M 2019-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.987 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.5 48.81 99.6 0.07 0.081 0.041 0.999 8.9 3.8 99767
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 95 1.586 1.846 0.933 0.333 3.8
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 4HYJ 1.5 20 94710 4991 99.56 0.1747 0.1734 0.1747 0.201 0.2009 RANDOM 27.433
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] -0.89 0.17 0.78 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.945 r_dihedral_angle_4_deg 21.957 r_dihedral_angle_3_deg 13.444 r_dihedral_angle_1_deg 5.664 r_angle_other_deg 1.25 r_angle_refined_deg 1.166 r_chiral_restr 0.065 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.945 r_dihedral_angle_4_deg 21.957 r_dihedral_angle_3_deg 13.444 r_dihedral_angle_1_deg 5.664 r_angle_other_deg 1.25 r_angle_refined_deg 1.166 r_chiral_restr 0.065 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3933 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 438
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing