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Lipidic sponge phase crystal structure of photosynthetic reaction centre from Blastochloris viridis (high dose)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PRC PDB ENTRY 2PRC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 8 MONOOLEIN WAS MIXED WITH WATER IN RATIO OF 60:40 (W/W) UNTIL A VISCOUS NON-BIREFRINGENT LCP WAS FORMED. THEREAFTER, LIPIDIC-SPONGE PHASE INITIATING SOLUTION (20% JEFFAMINE M600, 1M HEPES PH=8.0, 0.7M (NH4)2SO4 AND 2.5% 1,2,3-HEPTANETRIOL) WAS ADDED IN A RATIO OF 1 TO 4 (V/V) AND EQUILIBRATED UNTIL PHASE SEPARATION HAS OCCURRED. THE UPPER LIPIDIC-SPONGE PHASE WAS HARVESTED AND 1UL WAS USED AS A PRECIPITANT SOLUTION TOGETHER WITH 1UL OF 25 MG/ML PROTEIN SOLUTION IN A HANGING-DROP, VAPOUR-DIFFUSION EXPERIMENT. TO IMPROVE CRYSTAL QUALITY 1UL OF ADDITIVE 1M TRI-NA-CITRATE HAS BEEN ADDED TO THE CRYSTALLIZATION DROP.
Crystal Properties Matthews coefficient Solvent content 2.67 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.76 α = 90 b = 139.43 β = 90 c = 178.24 γ = 90
Symmetry Space Group P 21 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 100 PIXEL DECTRIS PILATUS 6M MIRRORS 2008-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 1.85 44.99 97.8 0.08 14.97 6.55 176119 2 32.5
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 1.85 2 92.1 0.48 3.72 6.74
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 2PRC 1.86 44.97 167284 8832 99.38 0.17185 0.17071 0.1751 0.19326 0.1958 RANDOM 29.528
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] -0.61 3.38 -2.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.822 r_dihedral_angle_4_deg 15.685 r_dihedral_angle_3_deg 12.389 r_dihedral_angle_1_deg 5.834 r_scangle_it 3.126 r_angle_refined_deg 2.253 r_scbond_it 2.216 r_mcangle_it 1.444 r_angle_other_deg 1.169 r_mcbond_it 0.962
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.822 r_dihedral_angle_4_deg 15.685 r_dihedral_angle_3_deg 12.389 r_dihedral_angle_1_deg 5.834 r_scangle_it 3.126 r_angle_refined_deg 2.253 r_scbond_it 2.216 r_mcangle_it 1.444 r_angle_other_deg 1.169 r_mcbond_it 0.962 r_mcbond_other 0.287 r_nbd_refined 0.244 r_nbd_other 0.205 r_nbtor_refined 0.188 r_symmetry_vdw_other 0.164 r_xyhbond_nbd_refined 0.157 r_symmetry_vdw_refined 0.144 r_chiral_restr 0.136 r_symmetry_hbond_refined 0.127 r_nbtor_other 0.088 r_metal_ion_refined 0.063 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_gen_planes_other 0.005 r_bond_other_d 0.002 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 9185 Nucleic Acid Atoms Solvent Atoms 692 Heterogen Atoms 713
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling AMoRE phasing