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1.96 A X-ray structure of photosynthetic reaction center from Rhodopseudomonas viridis:Crystals grown by microfluidic technique
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DXR PDB ENTRY 1DXR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 THE CRYSTALS WERE GROWN BY MICROFLUIDIC TECHNIQUE USING CRYSTALLIZATION BUFFER: 1.6 - 1.8 M (NH4)2SO4 IN TRIS PH 7.8. THE ADDITIVES WERE HEPTANETRIOL (3%, W/V) AND 2% TRIETHYL AMONIUM PHOSPHATE. THE DETERGENT WAS LAURYL DIMETHYLAMINE-N-OXIDE (LDA). THE PROTEIN COMPLEX WAS IN SODIUM PHOSPHATE BUFFER PH 6.0 AND 0.08% LDA.
Crystal Properties Matthews coefficient Solvent content 5 70
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 220.4 α = 90 b = 220.4 β = 90 c = 113.009 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD MARMOSAIC 300 mm CCD ADJUSTABLE FOCUSING MIRRORS 2006-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D APS 23-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 1.96 20 94.5 0.082 17.5 5.9 189189 24.5
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 1.96 2 67.4 0.48 2.3 4.1
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 (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 1DXR 1.96 20 189189 189189 9533 96.5 0.173 0.172 0.1783 0.19 0.1953 RANDOM 25.42
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] 0.35 0.35 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.902 r_dihedral_angle_4_deg 16.534 r_dihedral_angle_3_deg 12.261 r_dihedral_angle_1_deg 5.683 r_scangle_it 3.506 r_scbond_it 2.507 r_mcangle_it 1.659 r_angle_refined_deg 1.329 r_mcbond_it 1.117 r_angle_other_deg 1.055
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.902 r_dihedral_angle_4_deg 16.534 r_dihedral_angle_3_deg 12.261 r_dihedral_angle_1_deg 5.683 r_scangle_it 3.506 r_scbond_it 2.507 r_mcangle_it 1.659 r_angle_refined_deg 1.329 r_mcbond_it 1.117 r_angle_other_deg 1.055 r_mcbond_other 0.32 r_symmetry_vdw_refined 0.235 r_nbd_refined 0.224 r_symmetry_vdw_other 0.222 r_nbtor_refined 0.203 r_nbd_other 0.195 r_symmetry_hbond_refined 0.124 r_xyhbond_nbd_refined 0.114 r_nbtor_other 0.085 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9282 Nucleic Acid Atoms Solvent Atoms 771 Heterogen Atoms 970
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling