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Crystal Structure of S63A Variant of D-Dopachrome Tautomerase (D-DT)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DPT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M Tris pH 7.8, 24% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.99 38.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.498 α = 90 b = 94.267 β = 112.392 c = 91.465 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 90 PIXEL DECTRIS PILATUS3 S 6M 2024-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11583 ALS 8.3.1
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 1.529 94.27 99.62 0.997 7.19 6.7 177634
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 1.53 1.57 0.597
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 1.529 69.903 168658 8792 99.44 0.167 0.1657 0.1767 0.1961 0.2056 19.034
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] 0.001 -0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.036 r_dihedral_angle_4_deg 16.273 r_dihedral_angle_3_deg 12.326 r_dihedral_angle_1_deg 6.401 r_lrange_it 5.01 r_lrange_other 4.871 r_scangle_it 4.15 r_scangle_other 4.15 r_scbond_it 2.818 r_scbond_other 2.817
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.036 r_dihedral_angle_4_deg 16.273 r_dihedral_angle_3_deg 12.326 r_dihedral_angle_1_deg 6.401 r_lrange_it 5.01 r_lrange_other 4.871 r_scangle_it 4.15 r_scangle_other 4.15 r_scbond_it 2.818 r_scbond_other 2.817 r_angle_other_deg 2.502 r_mcangle_it 2.301 r_mcangle_other 2.301 r_angle_refined_deg 1.714 r_mcbond_it 1.645 r_mcbond_other 1.644 r_chiral_restr_other 1.297 r_symmetry_nbd_other 0.213 r_nbd_refined 0.211 r_nbd_other 0.194 r_nbtor_refined 0.162 r_symmetry_xyhbond_nbd_refined 0.16 r_xyhbond_nbd_refined 0.139 r_symmetry_nbd_refined 0.136 r_chiral_restr 0.12 r_symmetry_nbtor_other 0.075 r_symmetry_xyhbond_nbd_other 0.054 r_bond_other_d 0.035 r_gen_planes_other 0.014 r_bond_refined_d 0.012 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10418 Nucleic Acid Atoms Solvent Atoms 1065 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing