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Crystal structure of acetate:succinate CoA transferase (ASCT) from Trypanosoma brucei.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DLX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 0.05M HEPES-NaOH buffer pH 7.4, 18% (w/v) PEG 3350, 0.35M CaCl2
Crystal Properties Matthews coefficient Solvent content 2.22 44.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.886 α = 90 b = 164.635 β = 90 c = 187.573 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 PILATUS 2M-F 2019-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.00000 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.01 50 98.7 0.107 0.996 11.3 5.2 123547 31.4
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 2.01 2.13 97.3 0.564 0.698 2.5
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 3DLX 2.01 19.97 116411 6345 98.78 0.22797 0.22517 0.2308 0.27867 0.2799 RANDOM 32.452
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] 0.1 0.03 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.529 r_dihedral_angle_3_deg 18.059 r_dihedral_angle_4_deg 16.399 r_dihedral_angle_1_deg 7.492 r_long_range_B_refined 4.3 r_long_range_B_other 4.3 r_mcangle_it 2.547 r_mcangle_other 2.547 r_scangle_other 2.529 r_mcbond_it 1.594
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.529 r_dihedral_angle_3_deg 18.059 r_dihedral_angle_4_deg 16.399 r_dihedral_angle_1_deg 7.492 r_long_range_B_refined 4.3 r_long_range_B_other 4.3 r_mcangle_it 2.547 r_mcangle_other 2.547 r_scangle_other 2.529 r_mcbond_it 1.594 r_mcbond_other 1.594 r_scbond_it 1.569 r_scbond_other 1.569 r_angle_refined_deg 1.546 r_angle_other_deg 1.019 r_chiral_restr 0.094 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 14070 Nucleic Acid Atoms Solvent Atoms 370 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing