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Reaction centre from Rhodobacter sphaeroides strain R-26.1 complexed with brominated phosphatidylcholine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Unpublished structure of reaction centre at 1.95A resolution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, dioxane, Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature
16.0K
Crystal Properties Matthews coefficient Solvent content 5.54 77.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.844 α = 90 b = 139.844 β = 90 c = 184.335 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 ADSC QUANTUM 4 mirrors 2004-01-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 0.87 SRS PX9.6
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 2.7 34.36 99.9 0.082 14.6 5.8 57840 57.8
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 2.7 2.85 100 0.629 2.6 5.8 8353
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(Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Unpublished structure of reaction centre at 1.95A resolution 2.7 34.35 57529 54677 2852 99.66 0.16624 0.16624 0.16444 0.169 0.19944 0.2003 RANDOM 42.887
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] 0.3 0.15 0.3 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.671 r_dihedral_angle_4_deg 18.382 r_dihedral_angle_3_deg 15.748 r_dihedral_angle_1_deg 6.175 r_scangle_it 3.274 r_scbond_it 2.205 r_angle_refined_deg 1.856 r_mcangle_it 1.253 r_angle_other_deg 1.25 r_mcbond_it 0.674
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.671 r_dihedral_angle_4_deg 18.382 r_dihedral_angle_3_deg 15.748 r_dihedral_angle_1_deg 6.175 r_scangle_it 3.274 r_scbond_it 2.205 r_angle_refined_deg 1.856 r_mcangle_it 1.253 r_angle_other_deg 1.25 r_mcbond_it 0.674 r_symmetry_vdw_other 0.265 r_nbd_refined 0.226 r_symmetry_vdw_refined 0.224 r_symmetry_hbond_refined 0.218 r_nbd_other 0.202 r_nbtor_refined 0.2 r_xyhbond_nbd_refined 0.161 r_mcbond_other 0.148 r_chiral_restr 0.098 r_nbtor_other 0.093 r_metal_ion_refined 0.045 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 6468 Nucleic Acid Atoms Solvent Atoms 452 Heterogen Atoms 895
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing