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Crystal structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus, reduced, 2 mol/ASU, with bound NADH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FUG PDB ENTRY 2FUG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 0.1 M HEPES pH 7.5, 0.05 M NaCl, 0.1 M MgCl2, 7% PEG4000, 3 mM NADH, 5 mM sodium dithionite, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.17 61.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.002 α = 90 b = 151.015 β = 93.07 c = 216.624 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 CCD ADSC QUANTUM 315r 2007-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97654 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.1 29.913 88.2 0.151 0.151 7.4 2.6 111667 111667 62.81
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.27 90.2 0.586 0.586 1.4 2.6 16621
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 (All) 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 2FUG 3.1 29.571 114079 111667 2215 89.89 0.232 0.232 0.231 0.2261 0.262 0.2565 RANDOM 62.22
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] -7.678 3.523 -3.911 6.594
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 21.416 f_angle_d 1.375 f_chiral_restr 0.091 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 37316 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 290
Software Software Software Name Purpose SCALA data processing PHENIX refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling PHASER phasing SHARP phasing