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Crystal Structure of Delta 114-117 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 298 26-32% PEG 3350, 0.25-0.275M Ammonium Acetate.
Crystal Properties Matthews coefficient Solvent content 2.58 52.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.533 α = 90 b = 59.529 β = 107.93 c = 129.976 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 290 PIXEL DECTRIS PILATUS3 S 6M 2023-04-28 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) R Merge I (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 2.44 89.84 99.8 0.267 0.953 4.5 3.4 51582
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.44 2.48 99.7 1.363 0.25 1 3.5
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 2.44 89.84 51582 2702 99.65 0.25138 0.24878 0.2515 0.30177 0.2985 RANDOM 27.14
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] -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.268 r_dihedral_angle_4_deg 18.015 r_dihedral_angle_3_deg 17.944 r_dihedral_angle_1_deg 6.025 r_long_range_B_refined 4.861 r_long_range_B_other 4.86 r_mcangle_it 3.237 r_mcangle_other 3.237 r_scangle_other 2.965 r_angle_other_deg 2.541
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.268 r_dihedral_angle_4_deg 18.015 r_dihedral_angle_3_deg 17.944 r_dihedral_angle_1_deg 6.025 r_long_range_B_refined 4.861 r_long_range_B_other 4.86 r_mcangle_it 3.237 r_mcangle_other 3.237 r_scangle_other 2.965 r_angle_other_deg 2.541 r_mcbond_it 2.041 r_mcbond_other 2.041 r_scbond_it 1.836 r_scbond_other 1.836 r_angle_refined_deg 1.567 r_chiral_restr 0.066 r_bond_other_d 0.036 r_bond_refined_d 0.008 r_gen_planes_other 0.007 r_gen_planes_refined 0.006 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9380 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction PHENIX phasing