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Structure of apo TDO with a bound inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TIA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 5.3 mg/ml (124 uM) protein containing 2 mM AMT and 1 mM inhibitor
Reservoir solution: Morpheus II condition F8
5%(w/v) PEG 20K, 25%(w/v) 1,1,1-tris(hydroxymethyl)propane, 1%(w/v) NDSB 195,0.02M of each Monosaccharide II, 0.1M BES/TEA pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.44 49.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.738 α = 90 b = 132.906 β = 90 c = 137.495 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 6M 2023-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.00 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 3.08 76.31 95.2 0.171 0.056 0.998 9.8 9.8 27716
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.08 3.24 60.6 0.648 0.536 1.3 8.6
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 3.078 50.83 27708 1368 87 0.228 0.2267 0.2295 0.2519 0.252 RANDOM 83.64
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] 2.2922 -2.2458 -0.0465
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.41 t_omega_torsion 2.26 t_angle_deg 0.82 t_bond_d 0.007 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9839 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 156
Software Software Software Name Purpose BUSTER refinement autoPROC data reduction autoPROC data scaling PHASER phasing