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Bacterial Photosynthetic Reaction Center from Rhodobacter sphaeroides with ILE M265 replaced with THR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PCR PDB ENTRY 1PCR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 drop: 14 mg/mL protein, 0.8 M potassium phosphate, 5 mM Tris, 5 uM EDTA, 3.2% 1,2,3-heptanetriol, 2.0% dioxane, 140 mM sodium chloride, 0.045% LDAO, reservoir: 1.6 M potassium phosphate, cryoprotectant: 28% ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 5.66 78.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.87 α = 90 b = 138.87 β = 90 c = 185.49 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 300 mm CCD 2010-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D APS 21-ID-D
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 2.97 120.265 99.2 0.094 15.79 42919 -3 62.36
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 2.97 3.05 99.9 0.762 2.22
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 1PCR 2.97 19.77 42918 2146 100 0.174 0.174 0.1844 0.194 0.192 53.84
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] 0.18 0.09 0.18 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.22 r_dihedral_angle_4_deg 23.732 r_dihedral_angle_3_deg 22.442 r_dihedral_angle_1_deg 8.747 r_scangle_it 5.553 r_scbond_it 3.589 r_angle_refined_deg 3.196 r_mcangle_it 2.28 r_mcbond_it 1.212 r_chiral_restr 0.189
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.22 r_dihedral_angle_4_deg 23.732 r_dihedral_angle_3_deg 22.442 r_dihedral_angle_1_deg 8.747 r_scangle_it 5.553 r_scbond_it 3.589 r_angle_refined_deg 3.196 r_mcangle_it 2.28 r_mcbond_it 1.212 r_chiral_restr 0.189 r_bond_refined_d 0.035 r_gen_planes_refined 0.014 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6465 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 488
Software Software Software Name Purpose REFMAC refinement PHENIX refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing XSCALE data scaling