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Structure of LH2 from Rps. acidophila crystallized in lipidic mesophases
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NKZ PDB entry 1NKZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 293 200 microlitres of 40 %(w/w) protein, 0.05 %(w/v) LDAO, 20mM Tris/HCl and
60 %(w/w) monoolein mixed with 2 microlitres of precipitant: 20 %(w/v) pentaerythritol propoxylate, 0.1 M potassium formate, 0.1 M Tris/HCl, pH 8.0, Mesophase crystallization, lipidic cubic phase, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.61 65.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.443 α = 90 b = 126.384 β = 90 c = 129.705 γ = 90
Symmetry Space Group P 21 21 21
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 QUANTUM 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.9124 CHESS F1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.449 90.536 99.8 0.066 20.9 3.9 49999 49795
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.54 98.25 0.568 2.3 3.7 3208
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 1NKZ 2.45 10 49999 48989 2498 99.78 0.18651 0.18282 0.2032 0.25367 0.2609 RANDOM 41.842
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] 2.97 -4.14 1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.173 r_dihedral_angle_3_deg 18.044 r_dihedral_angle_4_deg 10.639 r_dihedral_angle_1_deg 8.963 r_scangle_it 4.217 r_scbond_it 2.866 r_mcangle_it 2.016 r_angle_refined_deg 1.414 r_mcbond_it 1.26 r_angle_other_deg 0.849
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.173 r_dihedral_angle_3_deg 18.044 r_dihedral_angle_4_deg 10.639 r_dihedral_angle_1_deg 8.963 r_scangle_it 4.217 r_scbond_it 2.866 r_mcangle_it 2.016 r_angle_refined_deg 1.414 r_mcbond_it 1.26 r_angle_other_deg 0.849 r_chiral_restr 0.784 r_metal_ion_refined 0.382 r_xyhbond_nbd_refined 0.353 r_nbd_refined 0.334 r_symmetry_hbond_refined 0.325 r_mcbond_other 0.319 r_nbd_other 0.247 r_symmetry_vdw_refined 0.232 r_nbtor_refined 0.195 r_symmetry_vdw_other 0.175 r_nbtor_other 0.101 r_bond_refined_d 0.03 r_gen_planes_other 0.019 r_gen_planes_refined 0.015 r_bond_other_d 0.005 r_xyhbond_nbd_other 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 6534 Nucleic Acid Atoms Solvent Atoms 613 Heterogen Atoms 2682
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing