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Lipidic cubic phase grown reaction centre from Rhodobacter sphaeroides, ground 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 2.8 55.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.142 α = 90 b = 100.142 β = 90 c = 238.002 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 ADSC CCD GE MIRROR 2004-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2.7 120 99.3 0.18 11.4 6.2 32255 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 2.7 2.79 100 0.79 2.1 6.3
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 2.7 39.53 32254 1696 99.4 0.212 0.21 0.2258 0.249 0.2567 RANDOM 31.19
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] -0.04 -0.04 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.583 r_angle_refined_deg 2.321 r_scangle_it 1.623 r_scbond_it 1.134 r_angle_other_deg 0.849 r_mcangle_it 0.693 r_mcbond_it 0.378 r_nbd_other 0.223 r_nbd_refined 0.193 r_symmetry_vdw_other 0.151
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.583 r_angle_refined_deg 2.321 r_scangle_it 1.623 r_scbond_it 1.134 r_angle_other_deg 0.849 r_mcangle_it 0.693 r_mcbond_it 0.378 r_nbd_other 0.223 r_nbd_refined 0.193 r_symmetry_vdw_other 0.151 r_xyhbond_nbd_refined 0.127 r_nbtor_other 0.085 r_chiral_restr 0.083 r_symmetry_vdw_refined 0.075 r_symmetry_hbond_refined 0.075 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 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 64 Heterogen Atoms 431
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling