☰ Navigation Tabs
L-threonine 3-Dehydrogenase from Trypanosoma cruzi (apo form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5L9A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291.15 25% PEG 3350, 200 mM ammonium acetate and 100 mM Bis-Tris pH 5.5
Crystal Properties Matthews coefficient Solvent content 1.976 37.781
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.685 α = 90 b = 81.834 β = 90.546 c = 83.674 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 2021-04-02 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 2.1 46.73 99.1 0.995 8.4 4.7 36424
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 2.1 2.16 98.6 0.595 4.5
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 2.1 46.727 36369 2004 98.719 0.203 0.1998 0.1998 0.2581 0.258 31.969
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] -0.286 1.531 1.449 -1.191
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.55 r_dihedral_angle_4_deg 19.416 r_dihedral_angle_3_deg 17.344 r_dihedral_angle_1_deg 7.192 r_lrange_it 6.577 r_lrange_other 6.559 r_scangle_it 4.567 r_scangle_other 4.565 r_mcangle_it 3.527 r_mcangle_other 3.526
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.55 r_dihedral_angle_4_deg 19.416 r_dihedral_angle_3_deg 17.344 r_dihedral_angle_1_deg 7.192 r_lrange_it 6.577 r_lrange_other 6.559 r_scangle_it 4.567 r_scangle_other 4.565 r_mcangle_it 3.527 r_mcangle_other 3.526 r_scbond_it 3.141 r_scbond_other 3.141 r_mcbond_it 2.384 r_mcbond_other 2.383 r_angle_other_deg 2.364 r_angle_refined_deg 1.744 r_nbd_other 0.25 r_symmetry_nbd_other 0.235 r_nbd_refined 0.233 r_symmetry_nbd_refined 0.227 r_nbtor_refined 0.187 r_chiral_restr 0.144 r_xyhbond_nbd_refined 0.143 r_symmetry_xyhbond_nbd_refined 0.11 r_symmetry_nbtor_other 0.087 r_symmetry_xyhbond_nbd_other 0.05 r_bond_other_d 0.035 r_bond_refined_d 0.014 r_gen_planes_other 0.008 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4977 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 2
Software Software Software Name Purpose MxCuBE data collection XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement Coot model building PDB_EXTRACT data extraction