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Reaction centre from Rhodobacter sphaeroides strain R-26.1 complexed with dibrominated phosphatidylglycerol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Unpublished structure of reaction centre at 1.95A resolution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 5.49 77.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.417 α = 90 b = 139.417 β = 90 c = 183.701 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 225 mm CCD mirrors 2005-03-18 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.9192 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 2.5 46.03 99.6 0.059 22.8 10.9 71485 59.6
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 2.64 99.4 0.543 4.6 11 10292
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(Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Unpublished structure of reaction centre at 1.95A resolution 2.5 46 71469 67921 3548 99.48 0.17347 0.17347 0.17223 0.1772 0.19677 0.1999 RANDOM 52.449
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] -0.71 -0.35 -0.71 1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.518 r_dihedral_angle_4_deg 18.137 r_dihedral_angle_3_deg 14.347 r_dihedral_angle_1_deg 5.86 r_scangle_it 3.24 r_scbond_it 2.293 r_angle_refined_deg 1.762 r_angle_other_deg 1.541 r_mcangle_it 1.324 r_mcbond_it 0.728
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.518 r_dihedral_angle_4_deg 18.137 r_dihedral_angle_3_deg 14.347 r_dihedral_angle_1_deg 5.86 r_scangle_it 3.24 r_scbond_it 2.293 r_angle_refined_deg 1.762 r_angle_other_deg 1.541 r_mcangle_it 1.324 r_mcbond_it 0.728 r_symmetry_vdw_other 0.271 r_symmetry_hbond_refined 0.27 r_nbd_refined 0.221 Cruickshank estimated coordinate error 0.203 r_nbd_other 0.201 r_nbtor_refined 0.197 r_mcbond_other 0.181 r_xyhbond_nbd_refined 0.178 r_symmetry_vdw_refined 0.157 r_chiral_restr 0.108 Maximum Likelihood estimated coordinate error 0.104 r_nbtor_other 0.093 r_metal_ion_refined 0.086 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_xyhbond_nbd_other 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6475 Nucleic Acid Atoms Solvent Atoms 410 Heterogen Atoms 818
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing