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Reaction centre from Rhodobacter sphaeroides strain R-26.1 complexed with dibrominated phosphatidylethanolamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Unpublished structure of reaction centre at 1.95A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 289 Potassium phosphate, LDAO, 1,2,3-heptanetriol, 1,2,3-hexanetriol, dioxane, NaCl, Tris-HCl, pH 8.0, VAPOR DIFFUSION,
SITTING DROP, temperature 16.0K
Crystal Properties Matthews coefficient Solvent content 5.48 77.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.289 α = 90 b = 139.289 β = 90 c = 183.839 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 CCD MARMOSAIC 225 mm CCD mirrors 2005-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.91929 ESRF BM14
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 2.75 46.03 99.9 0.066 23 10.9 54102 74.5
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 2.75 2.9 100 0.569 4.3 11.1 7805
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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(Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Unpublished structure of reaction centre at 1.95A resolution 2.75 46.01 54094 51405 2689 99.96 0.18369 0.18369 0.1817 0.1861 0.22193 0.2285 RANDOM 60.047
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] -0.2 -0.1 -0.2 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.48 r_dihedral_angle_4_deg 20.88 r_dihedral_angle_3_deg 16.568 r_dihedral_angle_1_deg 6.335 r_scangle_it 3.166 r_scbond_it 2.127 r_angle_refined_deg 1.878 r_angle_other_deg 1.274 r_mcangle_it 1.23 r_mcbond_it 0.676
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.48 r_dihedral_angle_4_deg 20.88 r_dihedral_angle_3_deg 16.568 r_dihedral_angle_1_deg 6.335 r_scangle_it 3.166 r_scbond_it 2.127 r_angle_refined_deg 1.878 r_angle_other_deg 1.274 r_mcangle_it 1.23 r_mcbond_it 0.676 r_symmetry_hbond_refined 0.372 Cruickshank estimated coordinate error 0.319 r_symmetry_vdw_other 0.303 r_nbd_refined 0.232 r_nbd_other 0.203 r_nbtor_refined 0.203 r_xyhbond_nbd_refined 0.182 Maximum Likelihood estimated coordinate error 0.152 r_symmetry_vdw_refined 0.144 r_mcbond_other 0.144 r_metal_ion_refined 0.135 r_chiral_restr 0.106 r_nbtor_other 0.093 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6494 Nucleic Acid Atoms Solvent Atoms 394 Heterogen Atoms 799
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing