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Crystal structure of porcine heart mitochondrial complex II bound with N-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, 7% PEG 4000, 200mM Sucrose, 100mM NaCl, 10mM CaCl2, 0.5mM EDTA, 3% 1,6-haxanediol, 0.5% n-decyl-beta-D-maltoside, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.59 65.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.465 α = 90 b = 84.065 β = 90 c = 294.622 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 2009-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98871 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 3.1 50 96.5 0.115 8.478 3.6 30528
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) 3.1 3.21 94.3 0.491 2.4 3.5 2907
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-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 3.139 47.62 30472 1536 95.347 0.2202 0.22 0.2678 0.2613 RANDOM 82.241
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] -0.174 0.64 -0.466
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.351 r_dihedral_angle_3_deg 17.033 r_dihedral_angle_4_deg 15.052 r_dihedral_angle_1_deg 4.666 r_angle_refined_deg 0.964 r_scangle_it 0.495 r_nbtor_refined 0.294 r_scbond_it 0.283 r_mcangle_it 0.245 r_nbd_refined 0.176
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.351 r_dihedral_angle_3_deg 17.033 r_dihedral_angle_4_deg 15.052 r_dihedral_angle_1_deg 4.666 r_angle_refined_deg 0.964 r_scangle_it 0.495 r_nbtor_refined 0.294 r_scbond_it 0.283 r_mcangle_it 0.245 r_nbd_refined 0.176 r_mcbond_it 0.13 r_symmetry_vdw_refined 0.118 r_xyhbond_nbd_refined 0.108 r_chiral_restr 0.067 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 185
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