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Crystal structure of porcine heart mitochondrial complex II bound with N-Biphenyl-3-yl-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 7.4 293 25mM HEPES-NAOH, 7% PEG 4000, 200mM Sucrose, 100mM NaCl, 10mM CaCl2, 0.5mM EDTA, 3% 1,6-haxanediol, 0.5% n-decyl-beta-D-maltoside, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.6 65.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.702 α = 90 b = 84.17 β = 90 c = 294.432 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 210 2007-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 3.2 50 99.8 0.076 19.333 4.8 29008
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 3.2 3.31 100 0.277 5.22 4.9 2822
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 3.24 37.63 28950 1474 98.71 0.206 0.203 0.2041 0.253 0.2526 RANDOM 70.868
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] 0.33 0.27 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.862 r_dihedral_angle_3_deg 18.073 r_dihedral_angle_4_deg 15.268 r_dihedral_angle_1_deg 4.961 r_angle_refined_deg 1.075 r_scangle_it 0.764 r_scbond_it 0.429 r_mcangle_it 0.323 r_mcbond_it 0.17 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.862 r_dihedral_angle_3_deg 18.073 r_dihedral_angle_4_deg 15.268 r_dihedral_angle_1_deg 4.961 r_angle_refined_deg 1.075 r_scangle_it 0.764 r_scbond_it 0.429 r_mcangle_it 0.323 r_mcbond_it 0.17 r_chiral_restr 0.075 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8480 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 191
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling