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Reaction centre from Rhodobacter sphaeroides strain R-26.1 complexed with dibrominated phosphatidylserine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Unpublished structure of reaction centre at 1.95A resolution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 5.47 77.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.355 α = 90 b = 139.355 β = 90 c = 183.217 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 2005-05-20 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 0.92 SRS PX10.1
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 3 39.29 99.7 0.085 15.3 6.9 41533 81.1
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 3 3.16 100 0.575 3.1 7 6031
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(Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Unpublished structure of reaction centre at 1.95A resolution 3 39.29 41494 39411 2083 99.43 0.17683 0.17683 0.17407 0.1785 0.22719 0.2249 RANDOM 57.076
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] -0.33 -0.17 -0.33 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.813 r_dihedral_angle_3_deg 17.15 r_dihedral_angle_4_deg 16.249 r_dihedral_angle_1_deg 6.5 r_scangle_it 2.788 r_angle_refined_deg 1.938 r_scbond_it 1.799 r_angle_other_deg 1.171 r_mcangle_it 1.118 r_mcbond_it 0.588
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.813 r_dihedral_angle_3_deg 17.15 r_dihedral_angle_4_deg 16.249 r_dihedral_angle_1_deg 6.5 r_scangle_it 2.788 r_angle_refined_deg 1.938 r_scbond_it 1.799 r_angle_other_deg 1.171 r_mcangle_it 1.118 r_mcbond_it 0.588 Cruickshank estimated coordinate error 0.502 r_symmetry_hbond_refined 0.336 r_nbd_refined 0.234 r_symmetry_vdw_other 0.232 r_symmetry_vdw_refined 0.222 r_nbtor_refined 0.207 r_nbd_other 0.205 Maximum Likelihood estimated coordinate error 0.192 r_xyhbond_nbd_refined 0.184 r_xyhbond_nbd_other 0.129 r_mcbond_other 0.108 r_metal_ion_refined 0.098 r_chiral_restr 0.093 r_nbtor_other 0.093 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6476 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 787
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing