☰ Navigation Tabs
Reaction centre from Rhodobacter sphaeroides strain R-26.1 complexed with dibrominated 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Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Unpublished structure of reaction centre at 1.95A resolution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, 1,2,3-hexanetriol, dioxane, NaCl, Tris-HCl, pH 8.0, VAPOR DIFFUSION,
SITTING DROP, temperature 16.0K
Crystal Properties Matthews coefficient Solvent content 5.5 77.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.543 α = 90 b = 139.543 β = 90 c = 183.965 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 0.91929 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 2.55 46.03 100 0.088 22.6 15.9 67857 54.2
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 2.55 2.69 100 0.538 5.8 16.1 9812
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(Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Unpublished structure of reaction centre at 1.95A resolution 2.55 46.03 67963 64601 3362 99.97 0.17986 0.17986 0.17824 0.1821 0.20984 0.2109 RANDOM 42.284
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] 0.72 0.36 0.72 -1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.082 r_dihedral_angle_4_deg 19.659 r_dihedral_angle_3_deg 14.826 r_dihedral_angle_1_deg 6.088 r_scangle_it 3.159 r_scbond_it 2.224 r_angle_refined_deg 1.758 r_mcangle_it 1.309 r_angle_other_deg 1.248 r_mcbond_it 0.727
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.082 r_dihedral_angle_4_deg 19.659 r_dihedral_angle_3_deg 14.826 r_dihedral_angle_1_deg 6.088 r_scangle_it 3.159 r_scbond_it 2.224 r_angle_refined_deg 1.758 r_mcangle_it 1.309 r_angle_other_deg 1.248 r_mcbond_it 0.727 r_symmetry_vdw_other 0.286 Cruickshank estimated coordinate error 0.227 r_nbd_refined 0.221 r_nbd_other 0.199 r_nbtor_refined 0.198 r_mcbond_other 0.182 r_symmetry_hbond_refined 0.178 r_xyhbond_nbd_refined 0.168 r_symmetry_vdw_refined 0.11 Maximum Likelihood estimated coordinate error 0.108 r_chiral_restr 0.104 r_metal_ion_refined 0.102 r_nbtor_other 0.091 r_xyhbond_nbd_other 0.053 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 6499 Nucleic Acid Atoms Solvent Atoms 477 Heterogen Atoms 855
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing