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Lipidic cubic phase grown reaction centre from Rhodobacter sphaeroides, excited state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OGV PDB ENTRY 1OGV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 7.5 60% MONOOLEIN/40% 25 MG/ML PROT. (4:1)18% JEFFAMINE M-600, 1M HEPES PH7.5, 0.7M AMM.SULF., pH 7.50
Crystal Properties Matthews coefficient Solvent content 3.03 59.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.099 α = 90 b = 100.099 β = 90 c = 237.02 γ = 90
Symmetry Space Group P 42 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 MARRESEARCH TOROIDAL MIRROR 2003-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID09 ESRF ID09
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 2.5 46.1 97.8 0.11 7.9 2.9 51049 2
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 2.5 2.59 98 0.71 1.7 3
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 1OGV 2.5 46.13 39236 2081 96.9 0.211 0.209 0.2321 0.247 0.2567 RANDOM 30.13
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] -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.611 r_angle_refined_deg 2.329 r_scangle_it 2.106 r_scbond_it 1.406 r_angle_other_deg 0.975 r_mcangle_it 0.897 r_mcbond_it 0.474 r_nbd_other 0.227 r_nbd_refined 0.198 r_symmetry_vdw_other 0.189
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.611 r_angle_refined_deg 2.329 r_scangle_it 2.106 r_scbond_it 1.406 r_angle_other_deg 0.975 r_mcangle_it 0.897 r_mcbond_it 0.474 r_nbd_other 0.227 r_nbd_refined 0.198 r_symmetry_vdw_other 0.189 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.129 r_symmetry_vdw_refined 0.113 r_nbtor_other 0.086 r_bond_refined_d 0.013 r_symmetry_hbond_refined 0.011 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined 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_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 6440 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 431
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling