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Crystal structure of porcine heart mitochondrial complex II bound with N-(3-Isopropoxy-phenyl)-phthalamicacid
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, 8% 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 3.56 65.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.119 α = 90 b = 84.12 β = 90 c = 293.558 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 270 2009-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.00000 Photon Factory BL-17A
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 3.4 50 98.7 0.132 8.518 3.6 24684
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) 3.4 3.52 100 0.555 2.34 3.5 2461
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 3.4 47.49 24598 1251 98.18 0.252 0.25 0.2517 0.299 0.3028 RANDOM 89.654
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] 0.02 0.08 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.839 r_dihedral_angle_3_deg 17.16 r_dihedral_angle_4_deg 15.067 r_dihedral_angle_1_deg 4.561 r_angle_refined_deg 0.948 r_scangle_it 0.332 r_mcangle_it 0.24 r_scbond_it 0.188 r_mcbond_it 0.131 r_chiral_restr 0.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.839 r_dihedral_angle_3_deg 17.16 r_dihedral_angle_4_deg 15.067 r_dihedral_angle_1_deg 4.561 r_angle_refined_deg 0.948 r_scangle_it 0.332 r_mcangle_it 0.24 r_scbond_it 0.188 r_mcbond_it 0.131 r_chiral_restr 0.063 r_bond_refined_d 0.006 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 181
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