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Crystal Structure of K109A 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 0.1M Sodium malonate pH 4.0, 12% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.15 42.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.723 α = 90 b = 94.45 β = 105.345 c = 95.253 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 6M 2024-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11584 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 1.43 94.45 99.95 0.998 9.9 6.6 229968
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 1.43 1.53 99.99 0.099
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 1.49 72.163 197304 10237 99.951 0.186 0.1848 0.1846 0.2165 0.2163 18.395
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 -0.003 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.891 r_dihedral_angle_4_deg 17.689 r_dihedral_angle_3_deg 12.216 r_dihedral_angle_1_deg 6.759 r_lrange_it 4.427 r_lrange_other 4.187 r_scangle_it 3.097 r_scangle_other 3.097 r_angle_other_deg 2.481 r_scbond_it 2.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.891 r_dihedral_angle_4_deg 17.689 r_dihedral_angle_3_deg 12.216 r_dihedral_angle_1_deg 6.759 r_lrange_it 4.427 r_lrange_other 4.187 r_scangle_it 3.097 r_scangle_other 3.097 r_angle_other_deg 2.481 r_scbond_it 2.129 r_scbond_other 2.129 r_mcangle_it 2.046 r_mcangle_other 2.046 r_angle_refined_deg 1.635 r_mcbond_it 1.501 r_mcbond_other 1.501 r_nbd_other 0.242 r_symmetry_nbd_refined 0.231 r_symmetry_nbd_other 0.218 r_nbd_refined 0.21 r_nbtor_refined 0.157 r_xyhbond_nbd_refined 0.131 r_symmetry_xyhbond_nbd_refined 0.131 r_chiral_restr 0.085 r_symmetry_nbtor_other 0.071 r_bond_other_d 0.035 r_symmetry_xyhbond_nbd_other 0.015 r_gen_planes_other 0.013 r_bond_refined_d 0.01 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10438 Nucleic Acid Atoms Solvent Atoms 1487 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing