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Mitochondrial rhodoquinol-fumarate reductase from the parasitic nematode Ascaris suum with the specific inhibitor 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 MICRODIALYSIS 8.4 293 15% (w/v) PEG 3350, 100mM Tris-HCl pH 8.4, 200mM NaCl, 1mM sodium malonate, 0.06% (w/v) C12E8, 0.04% (w/v) C12M
, MICRODIALYSIS, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.17 61.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.823 α = 90 b = 132.25 β = 90 c = 220.577 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 90 CCD ADSC QUANTUM 210 monochromator 2005-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1 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 3.4 50 90.2 0.105 8.1 4.2 43385 42027 -1
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 3.4 3.46 63.1 0.523 1.34 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3.44 49.72 43385 41132 2217 100 0.20929 0.20537 0.203 0.2814 0.2777 RANDOM 107.93
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] -0.11 -0.3 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.672 r_dihedral_angle_3_deg 24.142 r_dihedral_angle_4_deg 21.16 r_dihedral_angle_1_deg 7.563 r_scangle_it 2.178 r_angle_refined_deg 1.801 r_scbond_it 1.238 r_mcangle_it 1.078 r_mcbond_it 0.572 r_chiral_restr 0.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.672 r_dihedral_angle_3_deg 24.142 r_dihedral_angle_4_deg 21.16 r_dihedral_angle_1_deg 7.563 r_scangle_it 2.178 r_angle_refined_deg 1.801 r_scbond_it 1.238 r_mcangle_it 1.078 r_mcbond_it 0.572 r_chiral_restr 0.118 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17884 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 378
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling