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Crystal structure of cyanide-insensitive alternative oxidase from Trypanosoma brucei with ascofuranone derivative
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VV9 PDB ENTRY 3VV9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 30% PEG 400, 0.1M IMIDAZOLE, 0.5M POTASSIUM FORMATE, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.2 61.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.308 α = 90 b = 219.682 β = 114.89 c = 63.481 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 MX225HE 2010-07-16 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 2.59 50 93.4 0.124 8.6 2.5 57960 54110 -3
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 2.59 2.64 85.3 0.614 1.3
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 3VV9 2.59 39.81 54110 51307 2725 92.24 0.21593 0.2138 0.2195 0.25575 0.266 RANDOM 42.779
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] 32.86 -3.26 -44.49 11.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.734 r_dihedral_angle_3_deg 20.056 r_dihedral_angle_4_deg 16.699 r_dihedral_angle_1_deg 5.716 r_scangle_it 1.936 r_angle_refined_deg 1.321 r_scbond_it 1.228 r_mcangle_it 0.817 r_mcbond_it 0.449 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.734 r_dihedral_angle_3_deg 20.056 r_dihedral_angle_4_deg 16.699 r_dihedral_angle_1_deg 5.716 r_scangle_it 1.936 r_angle_refined_deg 1.321 r_scbond_it 1.228 r_mcangle_it 0.817 r_mcbond_it 0.449 r_chiral_restr 0.091 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 8637 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 108
Software Software Software Name Purpose SPACE data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling