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Crystal structure of the oxidized respiratory complex I subunit NuoEF from Aquifex aeolicus, mutation V90P(NuoE)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HL2 A,B of the search model were independently placed two times in the ASU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Tris pH 6.8-7.1, 0.8-1.05 M Na3Citrat, 0.1 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.69 54.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.246 α = 90 b = 64.326 β = 106.347 c = 121.576 γ = 90
Symmetry Space Group P 1 21 1
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 2012-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0000 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.84 116.661 99.7 0.071 0.083 0.042 0.998 13.7 3.7 122759
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.84 2.06 99.9 0.461 0.539 0.275 0.857 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.844 116.661 122736 6164 99.634 0.169 0.1678 0.1794 0.1899 0.1998 Random selection 27.11
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] -0.714 -1.322 0.391 0.938
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.367 r_dihedral_angle_3_deg 12.037 r_dihedral_angle_1_deg 5.92 r_dihedral_angle_2_deg 5.918 r_lrange_it 4.84 r_lrange_other 4.771 r_scangle_other 3.57 r_scangle_it 3.569 r_mcangle_it 2.285 r_mcangle_other 2.285
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.367 r_dihedral_angle_3_deg 12.037 r_dihedral_angle_1_deg 5.92 r_dihedral_angle_2_deg 5.918 r_lrange_it 4.84 r_lrange_other 4.771 r_scangle_other 3.57 r_scangle_it 3.569 r_mcangle_it 2.285 r_mcangle_other 2.285 r_scbond_other 2.163 r_scbond_it 2.162 r_mcbond_it 1.484 r_mcbond_other 1.484 r_angle_refined_deg 1.309 r_angle_other_deg 0.456 r_nbd_refined 0.208 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.143 r_metal_ion_refined 0.143 r_nbd_other 0.131 r_symmetry_xyhbond_nbd_refined 0.104 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.069 r_symmetry_nbd_refined 0.056 r_chiral_restr_other 0.024 r_symmetry_xyhbond_nbd_other 0.022 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9082 Nucleic Acid Atoms Solvent Atoms 592 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing