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Crystal structure of porcine heart mitochondrial complex II bound with Atpenin A5
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, 5% 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 3.53 65.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.751 α = 90 b = 83.841 β = 90 c = 293.735 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 2008-12-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 0.80000 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 95.7 0.079 15.657 3.8 27959
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) 3.2 3.31 97.4 0.488 2.4 3.7 2770
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 3.22 48.96 27888 1436 95.28 0.235 0.232 0.2284 0.282 0.2786 RANDOM 106.185
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] 0.71 0.09 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.032 r_dihedral_angle_3_deg 19.184 r_dihedral_angle_4_deg 17.217 r_dihedral_angle_1_deg 5.477 r_angle_refined_deg 1.11 r_scangle_it 0.839 r_scbond_it 0.481 r_mcangle_it 0.463 r_mcbond_it 0.248 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.032 r_dihedral_angle_3_deg 19.184 r_dihedral_angle_4_deg 17.217 r_dihedral_angle_1_deg 5.477 r_angle_refined_deg 1.11 r_scangle_it 0.839 r_scbond_it 0.481 r_mcangle_it 0.463 r_mcbond_it 0.248 r_chiral_restr 0.078 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8480 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 138
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