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Crystal structure of porcine heart mitochondrial complex II bound with N-(3-Pentafluorophenyloxy-phenyl)-2-trifluoromethyl-benzamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZOY PDB ENTRY 1ZOY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 293 25mM HEPES-NAOH, 6% PEG 4000, 200mM Sucrose, 100mM NaCl, 10mM CaCl2, 0.5mM EDTA, 3% 1,6-haxanediol, 0.5% n-decyl-beta-D-maltoside, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.67 66.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.609 α = 90 b = 84.249 β = 90 c = 295.646 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 315 2008-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.00000 SPring-8 BL41XU
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 3.3 50 98.2 0.08 12.783 4 27349
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 3.3 3.42 99.4 0.466 1.98 4.1 2716
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT PDB ENTRY 1ZOY 3.31 37.76 27275 1367 97.83 0.259 0.257 0.2563 0.307 0.305 RANDOM 124.638
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] 1.69 -0.48 -1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.628 r_dihedral_angle_3_deg 15.482 r_dihedral_angle_4_deg 10.189 r_dihedral_angle_1_deg 4.045 r_angle_refined_deg 0.867 r_mcangle_it 0.216 r_scangle_it 0.198 r_mcbond_it 0.12 r_scbond_it 0.111 r_chiral_restr 0.055
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.628 r_dihedral_angle_3_deg 15.482 r_dihedral_angle_4_deg 10.189 r_dihedral_angle_1_deg 4.045 r_angle_refined_deg 0.867 r_mcangle_it 0.216 r_scangle_it 0.198 r_mcbond_it 0.12 r_scbond_it 0.111 r_chiral_restr 0.055 r_bond_refined_d 0.005 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8480 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 197
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing