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Crystal structure of alternative oxidase from Trypanosoma brucei brucei complexed with cumarin derivative-17b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VV9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 30% PEG 400, 0.1M IMIDAZOLE, 0.5M POTASSIUM FORMATE
Crystal Properties Matthews coefficient Solvent content 3.15 60.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.218 α = 90 b = 221.812 β = 114.64 c = 62.611 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 CCD RAYONIX MX300HE 2014-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9000 SPring-8 BL44XU
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 98.8 0.074 8.4 3.1 32521
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 3.2 3.26 98.7 0.752 1.37 3
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 3VV9 3.2 42.19 26326 1418 90.88 0.19472 0.19157 0.1948 0.25248 0.2535 RANDOM
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] -10.23 20.91 -13.27 23.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.582 r_dihedral_angle_3_deg 21.094 r_dihedral_angle_4_deg 15.825 r_long_range_B_refined 11.637 r_long_range_B_other 11.633 r_mcangle_it 8.254 r_mcangle_other 8.253 r_scangle_other 7.877 r_dihedral_angle_1_deg 7.678 r_mcbond_it 5.243
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.582 r_dihedral_angle_3_deg 21.094 r_dihedral_angle_4_deg 15.825 r_long_range_B_refined 11.637 r_long_range_B_other 11.633 r_mcangle_it 8.254 r_mcangle_other 8.253 r_scangle_other 7.877 r_dihedral_angle_1_deg 7.678 r_mcbond_it 5.243 r_mcbond_other 5.239 r_scbond_it 4.927 r_scbond_other 4.912 r_angle_refined_deg 1.771 r_angle_other_deg 1.135 r_chiral_restr 0.099 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 8584 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing