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Avian mitochondrial complex II with Atpenin A5 bound, sidechain outside
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 7.5 277 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 Atpenin A5 after crystallization
Crystal Properties Matthews coefficient Solvent content 3.6 65.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.68 α = 90 b = 84.424 β = 90 c = 293.019 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 2007-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.000 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 2.37 38.83 99.7 0.156 7.7 9.07 73996 44.58
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 2.37 2.44 99.4 1.116 1.7 7.97
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 2.37 38.75 1.33 72805 2144 99.3 0.212 0.211 0.2133 0.237 0.2385 random 74.4621
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 10.013 f_angle_d 0.547 f_chiral_restr 0.039 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8494 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 379
Software Software Software Name Purpose PHENIX refinement DENZO data reduction SCALEPACK data scaling PHENIX phasing