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Bacterial Photosynthetic Reaction Center from Rhodobacter sphaeroides with ILE M265 replaced with ASN
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 7.5 298 drop: 13 mg/mL protein, 0.8 M potassium phosphate, 5 mM Tris, 5 uM EDTA, 4.0% 1,2,3-heptanetriol, 2.0% dioxane, 140 mM sodium chloride, 0.045% LDAO, reservoir: 1.6 M potassium phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 5.68 78.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.72 α = 90 b = 139.72 β = 90 c = 183.98 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 2012-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G APS 21-ID-G
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 2.93 121.001 99.6 0.125 13.37 45001 -3 55.99
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 2.93 3.01 100 0.793 2.89
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 2.93 121 44997 2250 99.6 0.187 0.185 0.1873 0.226 0.2273 48.49
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] -0.03 -0.01 -0.03 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.199 r_dihedral_angle_4_deg 23.924 r_dihedral_angle_3_deg 21.08 r_dihedral_angle_1_deg 7.376 r_scangle_it 3.655 r_angle_refined_deg 2.364 r_scbond_it 2.306 r_mcangle_it 1.558 r_mcbond_it 0.806 r_chiral_restr 0.138
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.199 r_dihedral_angle_4_deg 23.924 r_dihedral_angle_3_deg 21.08 r_dihedral_angle_1_deg 7.376 r_scangle_it 3.655 r_angle_refined_deg 2.364 r_scbond_it 2.306 r_mcangle_it 1.558 r_mcbond_it 0.806 r_chiral_restr 0.138 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 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 6391 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 507
Software Software Software Name Purpose REFMAC refinement PHENIX refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing XSCALE data scaling