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D-Dopachrome Tautomerase with 4-Hydroxyphenylpyruvate Bound in Catalytic Site at Atomic (0.98 Angstrom) Resolution
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 5.9 293 0.2M Ammonium Acetate, 0.1M Sodium Citrate pH 5.9, 28% PEG 4000 - soaked into 0.2M Ammonium Acetate, 0.1M Sodium Citrate pH 5.9, 33% PEG 4000, 600mM 4-Hydroxyphenylpyruvate
Crystal Properties Matthews coefficient Solvent content 2.17 43.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.765 α = 90 b = 83.765 β = 90 c = 40.535 γ = 120
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 2024-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 0.88557 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 0.98 72.54 99.1 0.04 0.042 0.013 1 23.1 9.5 178449
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.98 1 84.8 1.24 1.368 0.554 0.548 5.4
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 0.985 72.54 178351 8881 99.086 0.133 0.1321 0.1467 0.1416 13.706
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] 0.014 0.014 -0.029
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 39.724 r_dihedral_angle_2_deg 28.192 r_scbond_it 19.313 r_scbond_other 19.306 r_dihedral_angle_4_deg 15.591 r_scangle_it 13.378 r_scangle_other 13.375 r_dihedral_angle_3_deg 11.539 r_mcangle_it 10.867 r_mcangle_other 10.865
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 39.724 r_dihedral_angle_2_deg 28.192 r_scbond_it 19.313 r_scbond_other 19.306 r_dihedral_angle_4_deg 15.591 r_scangle_it 13.378 r_scangle_other 13.375 r_dihedral_angle_3_deg 11.539 r_mcangle_it 10.867 r_mcangle_other 10.865 r_mcbond_other 10.744 r_mcbond_it 10.737 r_lrange_it 10.216 r_lrange_other 10.187 r_dihedral_angle_1_deg 5.1 r_chiral_restr_other 2.784 r_angle_other_deg 2.622 r_angle_refined_deg 1.671 r_symmetry_xyhbond_nbd_refined 0.357 r_nbd_other 0.28 r_nbd_refined 0.239 r_symmetry_nbd_other 0.218 r_symmetry_nbd_refined 0.193 r_nbtor_refined 0.167 r_chiral_restr 0.115 r_xyhbond_nbd_refined 0.11 r_metal_ion_refined 0.106 r_ncsr_local_group_3 0.099 r_ncsr_local_group_2 0.085 r_ncsr_local_group_1 0.076 r_symmetry_nbtor_other 0.075 r_bond_other_d 0.035 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2635 Nucleic Acid Atoms Solvent Atoms 496 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing