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Crystal structure of ASCT D62N mutant from Trypanosoma brucei in complex with succinyl-CoA and acetylacetone.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LP1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 0.05M HEPES-NAOH BUFFER, 18% (W/V) PEG 3350, 0.35M CACL2
Crystal Properties Matthews coefficient Solvent content 2.32 46.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.222 α = 90 b = 164.833 β = 90 c = 189.395 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 PIXEL DECTRIS EIGER X 16M 2022-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.900000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.6 50 99.1 0.997 12.6 6.6 59146
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.75 99.1 0.897
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.6 20 55724 2968 99.15 0.21182 0.20737 0.2103 0.29575 0.2921 RANDOM 50.989
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.362 r_long_range_B_refined 9.198 r_long_range_B_other 9.198 r_dihedral_angle_2_deg 8.927 r_dihedral_angle_1_deg 7.752 r_scangle_other 6.845 r_mcangle_it 5.822 r_mcangle_other 5.822 r_scbond_it 4.309 r_scbond_other 4.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.362 r_long_range_B_refined 9.198 r_long_range_B_other 9.198 r_dihedral_angle_2_deg 8.927 r_dihedral_angle_1_deg 7.752 r_scangle_other 6.845 r_mcangle_it 5.822 r_mcangle_other 5.822 r_scbond_it 4.309 r_scbond_other 4.308 r_mcbond_it 3.74 r_mcbond_other 3.739 r_angle_refined_deg 1.63 r_angle_other_deg 0.558 r_chiral_restr 0.076 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 14193 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing