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Crystal structure of Thermoplasmatales archaeon heliorhodopsin E108D mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6IS6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 5 293 25% PEG 350 MME, 100mM Na-citrate, 100mM ammonium sulfate or lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.56 51.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.86 α = 90 b = 72.86 β = 90 c = 115.05 γ = 90
Symmetry Space Group P 42 21 2
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 2019-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.000 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.6 30 99.1 0.38 0.982 5.36 7.71 9975
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.76 98.6 1.806 0.484 1.04 7.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6is6 2.6 28.368 9975 502 99.096 0.225 0.2215 0.2307 0.2834 0.2938 36.753
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] -0.017 -0.017 0.033
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.561 r_dihedral_angle_3_deg 18.287 r_dihedral_angle_4_deg 15.758 r_lrange_it 6.992 r_lrange_other 6.991 r_dihedral_angle_1_deg 5.284 r_scangle_it 3.25 r_scangle_other 3.249 r_mcangle_it 3.158 r_mcangle_other 3.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.561 r_dihedral_angle_3_deg 18.287 r_dihedral_angle_4_deg 15.758 r_lrange_it 6.992 r_lrange_other 6.991 r_dihedral_angle_1_deg 5.284 r_scangle_it 3.25 r_scangle_other 3.249 r_mcangle_it 3.158 r_mcangle_other 3.156 r_scbond_it 1.988 r_scbond_other 1.987 r_mcbond_other 1.885 r_mcbond_it 1.884 r_angle_refined_deg 1.359 r_angle_other_deg 1.166 r_symmetry_xyhbond_nbd_refined 0.435 r_symmetry_nbd_refined 0.249 r_nbd_refined 0.188 r_xyhbond_nbd_refined 0.179 r_nbtor_refined 0.175 r_symmetry_nbd_other 0.174 r_nbd_other 0.173 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.065 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2007 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 250
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing