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Crystal Structure of T115A Variant of D-Dopachrome Tautomerase (D-DT) Bound to 4CPPC
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 28-30% PEG 4000, 0.1M Sodium Citrate pH 5.8-6.2, 0.2M Ammonium Acetate
Crystal Properties Matthews coefficient Solvent content 2.1 41.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.952 α = 90 b = 81.952 β = 90 c = 40.804 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 280 PIXEL DECTRIS PILATUS3 S 6M 2022-08-13 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) 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 1.33 40.98 97.2 0.046 0.051 0.022 0.999 22.4 5.1 22799
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 1.33 1.35 93.9 0.238 0.265 0.115 0.945 5.1
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 1.33 40.98 21599 1200 97.21 0.1068 0.10507 0.1108 0.13897 0.1415 RANDOM 13.808
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.497 r_dihedral_angle_4_deg 24.337 r_dihedral_angle_3_deg 11.572 r_rigid_bond_restr 8.306 r_dihedral_angle_1_deg 4.948 r_scangle_other 3.814 r_long_range_B_other 3.515 r_long_range_B_refined 3.513 r_scbond_other 3.41 r_scbond_it 3.406
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.497 r_dihedral_angle_4_deg 24.337 r_dihedral_angle_3_deg 11.572 r_rigid_bond_restr 8.306 r_dihedral_angle_1_deg 4.948 r_scangle_other 3.814 r_long_range_B_other 3.515 r_long_range_B_refined 3.513 r_scbond_other 3.41 r_scbond_it 3.406 r_mcangle_other 1.893 r_mcangle_it 1.892 r_angle_other_deg 1.887 r_mcbond_it 1.763 r_angle_refined_deg 1.729 r_mcbond_other 1.509 r_chiral_restr 0.091 r_bond_other_d 0.018 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_gen_planes_other 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 874 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement xia2 data scaling MOLREP phasing XDS data reduction