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Crystal structure of new trigonal form of photosynthetic reaction center from Blastochloris viridis. Crystals grown in microfluidics by detergent capture.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I5N PDB entry 2I5N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Plug-based Microfluidics 6 296 9 mg/mL Protein, 4.6 mM LDAO, 10 mM Methyl-beta-cyclodextrin, 1.6-1.7 M Sulfate, 4.5% w/v Triethylammonium phosphate pH 6.0, 3% 1,2,3-heptanetriol, 30 mM NaH2PO4-Na2HPO4 pH 6.0, Plug-based Microfluidics, temperature 296K
Crystal Properties Matthews coefficient Solvent content 7.19 82.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 241.171 α = 90 b = 241.171 β = 90 c = 113.391 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 100 CCD MARMOSAIC 300 mm CCD 2008-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.2 50 99.8 0.168 30.3 6 62037 62037
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 PDB entry 2I5N 3.21 50 62025 3145 99.58 0.194 0.192 0.1958 0.224 0.2277 RANDOM 67.435
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] 3.88 1.94 3.88 -5.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.642 r_dihedral_angle_3_deg 17.749 r_dihedral_angle_4_deg 15.265 r_dihedral_angle_1_deg 5.634 r_scangle_it 2.275 r_angle_refined_deg 1.437 r_scbond_it 1.302 r_mcangle_it 1.073 r_mcbond_it 0.552 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.642 r_dihedral_angle_3_deg 17.749 r_dihedral_angle_4_deg 15.265 r_dihedral_angle_1_deg 5.634 r_scangle_it 2.275 r_angle_refined_deg 1.437 r_scbond_it 1.302 r_mcangle_it 1.073 r_mcbond_it 0.552 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9282 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 870
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing