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Crystal structure of R. sphaeroides Photosynthetic Reaction Center variant; Y(M210)3-methyltyrosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J8C Chloro coordiante
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 1 M potassium phosphate, 3.5% 1,2,3-heptanetriol, and 0.1% LDAO precipitant solution; 1.4-1.5 M potassium phosphate reservoir solution, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 5.65 78.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.96 α = 90 b = 140.96 β = 90 c = 187.01 γ = 120
Symmetry Space Group P 31 2 1
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 EIGER X 16M Rh coated collimating mirror, Toroidal focusing mirror 2018-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 1.19499 SSRL BL14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.75 38.96 99.7 0.15 0.16 0.998 11.39 8.526 56220 63.009
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.82 100 1.422 1.512 0.649 1.67 8.743
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 Chloro coordiante 2.75 38.96 53409 2811 99.73 0.1799 0.1788 0.1855 0.2014 0.2038 RANDOM 61.351
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] 0.55 0.28 0.55 -1.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.516 r_dihedral_angle_3_deg 15.107 r_dihedral_angle_4_deg 15.096 r_dihedral_angle_1_deg 6.49 r_angle_refined_deg 2.139 r_angle_other_deg 1.137 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.516 r_dihedral_angle_3_deg 15.107 r_dihedral_angle_4_deg 15.096 r_dihedral_angle_1_deg 6.49 r_angle_refined_deg 2.139 r_angle_other_deg 1.137 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6459 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 627
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction PHASER phasing