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Crystal structure of R. sphaeroides Photosynthetic Reaction Center variant; Y(M210)3-chlorotyrosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J8C
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 Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.674 α = 90 b = 141.674 β = 90 c = 187.419 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 250 PIXEL DECTRIS PILATUS3 S 6M 2017-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97893 SSRL BL9-2
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 2.3 39.11 94.8 0.115 0.127 0.996 9.8 5.276 91797 54.371
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 2.3 2.36 95.8 1.187 1.317 0.553 1.57 5.199
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 2j8c 2.3 39.11 86659 4508 94.11 0.1579 0.1571 0.165 0.1742 0.1785 RANDOM 45.21
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] 0.09 0.04 0.09 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.939 r_dihedral_angle_4_deg 17.922 r_dihedral_angle_3_deg 13.743 r_dihedral_angle_1_deg 6.204 r_angle_refined_deg 2.167 r_angle_other_deg 1.212 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.939 r_dihedral_angle_4_deg 17.922 r_dihedral_angle_3_deg 13.743 r_dihedral_angle_1_deg 6.204 r_angle_refined_deg 2.167 r_angle_other_deg 1.212 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6466 Nucleic Acid Atoms Solvent Atoms 313 Heterogen Atoms 628
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction MOLREP phasing