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Crystal structure of Blastochloris viridis heterodimer mutant reaction center
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 MICROBATCH 6 298 Plug-based microfluidics, Precipitant was mixed with buffer and RC sample in a microfluidic chip. The final precipitant concentration was ~1.7 M ammonium sulfate, 0.1% LDAO,30 mM NaH2PO4-Na2HPO4, pH 6.0, 3% 1,2,3-heptanetriol, 1.9% triethylammonium phosphate. RC concentration was ~ 9.4 mg/mL, Microbatch, temperature 298K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 220.132 α = 90 b = 220.132 β = 90 c = 112.744 γ = 90
Symmetry Space Group P 43 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 CCD ADSC QUANTUM 315 2007-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C APS 14-BM-C
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 2.5 50 0.137 7.1 95377
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 0.709 6.2
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 2.5 20 90386 4765 99.21 0.17726 0.17574 0.1752 0.20556 0.2046 RANDOM 31.995
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] 0.34 0.34 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.108 r_dihedral_angle_4_deg 17.105 r_dihedral_angle_3_deg 14.436 r_dihedral_angle_1_deg 5.626 r_scangle_it 2.672 r_scbond_it 1.76 r_angle_refined_deg 1.503 r_mcangle_it 1.186 r_mcbond_it 0.667 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.108 r_dihedral_angle_4_deg 17.105 r_dihedral_angle_3_deg 14.436 r_dihedral_angle_1_deg 5.626 r_scangle_it 2.672 r_scbond_it 1.76 r_angle_refined_deg 1.503 r_mcangle_it 1.186 r_mcbond_it 0.667 r_nbtor_refined 0.314 r_symmetry_vdw_refined 0.251 r_nbd_refined 0.21 r_symmetry_hbond_refined 0.144 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9278 Nucleic Acid Atoms Solvent Atoms 730 Heterogen Atoms 909
Software Software Software Name Purpose HKL-2000 data collection CCP4 model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CCP4 phasing