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Reaction centre from Rhodobacter sphaeroides strain R-26.1 complexed with tetrabrominated 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Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Unpublished structure of reaction centre at 1.95A resolution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 5.52 77.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.554 α = 90 b = 139.554 β = 90 c = 184.609 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 2004-05-11 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 2.45 39.37 99.7 0.068 18 8.6 76588 51.5
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 2.45 2.58 100 0.614 3.8 7.8 11112
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(Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Unpublished structure of reaction centre at 1.95A resolution 2.45 39.36 75227 71518 3709 97.96 0.18035 0.18035 0.1788 0.1831 0.20914 0.2111 RANDOM 44.677
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] 0.86 0.43 0.86 -1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.208 r_dihedral_angle_4_deg 18.081 r_dihedral_angle_3_deg 14.632 r_dihedral_angle_1_deg 5.892 r_scangle_it 3.307 r_scbond_it 2.33 r_angle_refined_deg 1.738 r_mcangle_it 1.353 r_angle_other_deg 1.244 r_mcbond_it 0.751
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.208 r_dihedral_angle_4_deg 18.081 r_dihedral_angle_3_deg 14.632 r_dihedral_angle_1_deg 5.892 r_scangle_it 3.307 r_scbond_it 2.33 r_angle_refined_deg 1.738 r_mcangle_it 1.353 r_angle_other_deg 1.244 r_mcbond_it 0.751 r_symmetry_vdw_other 0.289 r_nbd_refined 0.221 r_nbd_other 0.201 r_symmetry_hbond_refined 0.201 Cruickshank estimated coordinate error 0.198 r_nbtor_refined 0.196 r_mcbond_other 0.195 r_symmetry_vdw_refined 0.188 r_xyhbond_nbd_refined 0.162 Maximum Likelihood estimated coordinate error 0.115 r_metal_ion_refined 0.108 r_chiral_restr 0.105 r_nbtor_other 0.092 r_xyhbond_nbd_other 0.039 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 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 441 Heterogen Atoms 853
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing