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Crystal structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus, oxidized, 4 mol/ASU, re-refined to 3.15 angstrom resolution
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, 0.4 M NaCl, 0.1 M CaCl2, 8% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.12 60.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.08 α = 90 b = 266.112 β = 104.71 c = 201.731 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 210 2004-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97564 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 3.15 30 92.3 0.18 0.18 6 3.2 218122 218122 69.08
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 3.15 3.32 89 0.759 0.759 1.2 3 30663
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 3.15 29.985 195404 195404 3881 82.53 0.238 0.238 0.237 0.2321 0.27 0.2616 RANDOM 72.78
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] -1.038 -0.079 -2.941 -1.89
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 21.691 f_angle_d 1.295 f_chiral_restr 0.09 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 74632 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 396
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling SHARP phasing DM phasing