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Crystal structure of Na(+)-translocating NADH-quinone reductase subunit C (YP_001302508.1) from Parabacteroides distasonis ATCC 8503 at 1.10 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 15.0000% Glycerol, 0.1700M NaOAc, 25.5000% PEG-4000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.15 42.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.444 α = 90 b = 60.693 β = 90 c = 82.758 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 MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2010-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
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 1.1 29.739 95.2 0.041 14.69 74185 -3 7.951
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 1.14 89.9 0.534 2.2
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.1 29.739 74143 3700 96 0.117 0.116 0.138 0.1519 RANDOM 13.424
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] 0.22 0.34 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.21 r_dihedral_angle_3_deg 10.886 r_dihedral_angle_4_deg 9.216 r_scangle_it 5.354 r_dihedral_angle_1_deg 4.249 r_scbond_it 3.71 r_mcangle_it 2.356 r_angle_other_deg 1.647 r_angle_refined_deg 1.474 r_mcbond_it 1.474
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.21 r_dihedral_angle_3_deg 10.886 r_dihedral_angle_4_deg 9.216 r_scangle_it 5.354 r_dihedral_angle_1_deg 4.249 r_scbond_it 3.71 r_mcangle_it 2.356 r_angle_other_deg 1.647 r_angle_refined_deg 1.474 r_mcbond_it 1.474 r_rigid_bond_restr 1.159 r_mcbond_other 0.859 r_chiral_restr 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1803 Nucleic Acid Atoms Solvent Atoms 411 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing