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Crystal Structure of I64A 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 0.125 M CaCl2, 15% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.34 47.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.522 α = 90 b = 151.769 β = 108.987 c = 91.49 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 2024-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.115840 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 1.539 86.512 99.18 0.998 10.33 6.6 303202
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 1.54 1.58 0.356
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 1.539 86.512 287837 15097 99.038 0.169 0.1678 0.1803 0.1983 0.2072 19.197
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 26.784 r_dihedral_angle_4_deg 18.142 r_dihedral_angle_3_deg 11.497 r_dihedral_angle_1_deg 6.543 r_lrange_it 5.087 r_lrange_other 4.691 r_scangle_it 3.718 r_scangle_other 3.718 r_scbond_it 2.523 r_scbond_other 2.523
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.784 r_dihedral_angle_4_deg 18.142 r_dihedral_angle_3_deg 11.497 r_dihedral_angle_1_deg 6.543 r_lrange_it 5.087 r_lrange_other 4.691 r_scangle_it 3.718 r_scangle_other 3.718 r_scbond_it 2.523 r_scbond_other 2.523 r_angle_other_deg 2.475 r_mcangle_it 2.113 r_mcangle_other 2.112 r_angle_refined_deg 1.62 r_mcbond_it 1.529 r_mcbond_other 1.529 r_nbd_other 0.257 r_nbd_refined 0.218 r_symmetry_nbd_other 0.218 r_symmetry_nbd_refined 0.175 r_nbtor_refined 0.16 r_xyhbond_nbd_refined 0.158 r_symmetry_xyhbond_nbd_refined 0.158 r_metal_ion_refined 0.09 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.07 r_symmetry_xyhbond_nbd_other 0.038 r_bond_other_d 0.035 r_gen_planes_other 0.013 r_bond_refined_d 0.011 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15639 Nucleic Acid Atoms Solvent Atoms 3180 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing