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Room temperature structure of the Rhodobacter Sphaeroides Photosynthetic Reaction Center F(M197)H mutant at 51 MPa helium gas pressure in a sapphire capillary
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V3Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 289 20-25 mg/ml protein solution was mixed 1:1 with lipid sponge phase. The mixture was filled into a sealed plastic tip covered with an excess amount of 1 M trisodium citrate and incubated in the dark at 289 K for 1 week.
Crystal Properties Matthews coefficient Solvent content 3.41 63.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.29 α = 90 b = 102.29 β = 90 c = 237.99 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 295 PIXEL DECTRIS PILATUS3 X CdTe 2M 2019-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 0.477 PETRA III, DESY P11
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 2.49 46.99 98.85 0.306 0.326 0.109 0.984 5.86 8.4 44663 40.43
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 2.49 2.579 99.18 2.105 2.266 0.818 0.347 1.01 7.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3V3Y 2.49 46.99 1.33 44643 1794 98.87 0.1782 0.1768 0.1771 0.212 0.2125 51.03
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.8974 f_angle_d 0.562 f_chiral_restr 0.0386 f_plane_restr 0.0034 f_bond_d 0.0027
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6466 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 689
Software Software Software Name Purpose Coot model building PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing