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X-ray high resolution structure of the photosynthetic reaction center from Rb. sphaeroides at pH 9 in the charge-separated state
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 9 pH 9
Crystal Properties Matthews coefficient Solvent content 4.81 74.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.46 α = 90 b = 139.46 β = 90 c = 184.73 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 MARRESEARCH MIRRORS 2003-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B EMBL/DESY, HAMBURG BW7B
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 2.2 50 98.1 0.1 10.29 2.5 103587 -3
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 2.2 2.3 89.2 0.43 3.72 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1PCR 2.21 50 100374 3110 99.1 0.203 0.202 0.1964 0.236 0.1891 RANDOM 43.65
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.008 r_scangle_it 3.725 r_scbond_it 2.529 r_angle_refined_deg 2.465 r_mcangle_it 1.714 r_mcbond_it 0.959 r_nbd_refined 0.218 r_symmetry_hbond_refined 0.21 r_symmetry_vdw_refined 0.179 r_xyhbond_nbd_refined 0.167
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.008 r_scangle_it 3.725 r_scbond_it 2.529 r_angle_refined_deg 2.465 r_mcangle_it 1.714 r_mcbond_it 0.959 r_nbd_refined 0.218 r_symmetry_hbond_refined 0.21 r_symmetry_vdw_refined 0.179 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.126 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6471 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 790
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling CNS phasing