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The crystal structure of the trypanosome alternative oxidase complexed with a trypanocidal phosphonium derivative (compound1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VVA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 30% PEG 400, 0.1 M IMIDAZOLE, 0.5M POTASSIUM FORMATE, PH 7.4
Crystal Properties Matthews coefficient Solvent content 3.86 68.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.368 α = 90 b = 221.727 β = 114.5 c = 62.855 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M 2017-12-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98000 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 3.01 50 92 0.071 6.3 2.8 35302
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.01 3.05 0.673 0.785 1.1
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 3VVA 3.01 44.96 28877 1491 81.8 0.1975 0.19452 0.1929 0.25353 0.246 RANDOM 67.637
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] -0.09 0.58 -0.1 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.911 r_dihedral_angle_3_deg 20.351 r_dihedral_angle_4_deg 16.708 r_long_range_B_refined 9.381 r_long_range_B_other 9.381 r_dihedral_angle_1_deg 8.514 r_mcangle_it 6.248 r_mcangle_other 6.248 r_scangle_other 5.385 r_mcbond_it 3.848
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.911 r_dihedral_angle_3_deg 20.351 r_dihedral_angle_4_deg 16.708 r_long_range_B_refined 9.381 r_long_range_B_other 9.381 r_dihedral_angle_1_deg 8.514 r_mcangle_it 6.248 r_mcangle_other 6.248 r_scangle_other 5.385 r_mcbond_it 3.848 r_mcbond_other 3.848 r_scbond_it 3.231 r_scbond_other 3.23 r_angle_refined_deg 1.619 r_angle_other_deg 1.174 r_chiral_restr 0.093 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8749 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing