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Avian mitochondrial complex II with thiapronil bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YQ3 PDB ENTRY 1YQ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 47 g/L PEG3350, 30 mL/L PEG400, 23 mL/L isopropanol, 0.05 M HEPES sodium, 0.01 M Tris-HCl, 3.1 mM manganese chloride, 0.62 mM magnesium chloride, 1.5 mM sodium azide, 0.25 mM sodium EDTA, 10 g/L octyl beta-D-glucoside, undecyl-beta-D-maltoside, crystal was soaked with thiapronil after crystallization
Crystal Properties Matthews coefficient Solvent content 3.64 66.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.361 α = 90 b = 84.622 β = 90 c = 293.337 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 315r 2007-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.00 ALS 8.2.2
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 2.145 51.52 90.2 0.108 4.6 3.1 89869 -3 47.32
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 2.15 2.21 42 0.604 1.1 2.21
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE PDB ENTRY 1YQ3 2.15 47.93 1.33 89446 2652 89.74 0.2187 0.2181 0.2196 0.238 0.2398 Random 70.61
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.0228 f_angle_d 0.7211 f_chiral_restr 0.044 f_plane_restr 0.0046 f_bond_d 0.0043
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8490 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 429
Software Software Software Name Purpose PHENIX refinement DENZO data reduction SCALEPACK data scaling PHENIX phasing