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L-threonine 3-Dehydrogenase from Trypanosoma cruzi in complex with NAD and acetate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8GIL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.3 291 0.2 M Ammonium acetate, 0.1 M Bis-Tris (pH 5.3), 25% PEG 3350, 25% glycerol.
Crystal Properties Matthews coefficient Solvent content 2.04 39.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.274 α = 90 b = 82.733 β = 90.446 c = 84.384 γ = 90
Symmetry Space Group P 1 21 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 2021-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS SIRIUS BEAMLINE MANACA 0.977180 LNLS SIRIUS MANACA
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 1.73 47.317 99.8 0.997 7.8 2 67241
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 1.73 1.77 99.3 0.466 2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.75 47.317 64898 3192 99.06 0.181 0.1797 0.1801 0.2096 0.2108 25.309
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] 1.106 0.937 -0.05 -1.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.661 r_dihedral_angle_4_deg 19.051 r_dihedral_angle_3_deg 14.04 r_lrange_it 7.079 r_dihedral_angle_1_deg 6.829 r_scangle_it 4.407 r_scbond_it 3.05 r_mcangle_it 2.755 r_mcbond_it 1.981 r_angle_refined_deg 1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.661 r_dihedral_angle_4_deg 19.051 r_dihedral_angle_3_deg 14.04 r_lrange_it 7.079 r_dihedral_angle_1_deg 6.829 r_scangle_it 4.407 r_scbond_it 3.05 r_mcangle_it 2.755 r_mcbond_it 1.981 r_angle_refined_deg 1.58 r_nbtor_refined 0.315 r_symmetry_nbd_refined 0.251 r_nbd_refined 0.216 r_symmetry_xyhbond_nbd_refined 0.165 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.107 r_metal_ion_refined 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4971 Nucleic Acid Atoms Solvent Atoms 285 Heterogen Atoms 124
Software Software Software Name Purpose MxCuBE data collection XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement Coot model building