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Lipidic sponge phase crystal structure of the photosynthetic reaction centre from Blastochloris viridis (low 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 = 84.45 α = 90 b = 138.498 β = 90 c = 177.77 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 CCD ADSC CCD MIRRORS 2007-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 1.95 45.9 96.2 0.09 10.9 4.3 152112 2 25.1
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 1.95 2.06 86.4 0.73 2.1 3.6
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 1.95 176.78 138487 7313 95.85 0.17446 0.17305 0.1859 0.20122 0.2131 RANDOM 26.466
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] -0.02 2.93 -2.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.385 r_dihedral_angle_4_deg 15.405 r_dihedral_angle_3_deg 13.104 r_dihedral_angle_1_deg 6.595 r_scangle_it 2.415 r_angle_refined_deg 2.09 r_scbond_it 1.732 r_mcangle_it 1.101 r_angle_other_deg 0.972 r_mcbond_it 0.707
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.385 r_dihedral_angle_4_deg 15.405 r_dihedral_angle_3_deg 13.104 r_dihedral_angle_1_deg 6.595 r_scangle_it 2.415 r_angle_refined_deg 2.09 r_scbond_it 1.732 r_mcangle_it 1.101 r_angle_other_deg 0.972 r_mcbond_it 0.707 r_nbd_refined 0.21 r_symmetry_hbond_refined 0.21 r_nbd_other 0.199 r_mcbond_other 0.191 r_nbtor_refined 0.189 r_symmetry_vdw_other 0.151 r_xyhbond_nbd_refined 0.137 r_symmetry_vdw_refined 0.124 r_chiral_restr 0.088 r_nbtor_other 0.088 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_gen_planes_other 0.004 r_bond_other_d 0.002 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_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 9187 Nucleic Acid Atoms Solvent Atoms 711 Heterogen Atoms 764
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing