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Crystal Structure of V113N Variant of D-Dopachrome Tautomerase (D-DT) Bound with 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 26-32% PEG 4000, 0.1M Sodium Citrate, 0.2M Ammonium Acetate
Crystal Properties Matthews coefficient Solvent content 2.33 47.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.093 α = 90 b = 111.093 β = 90 c = 66.07 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 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) 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 1.5 55.6 99.1 0.233 0.239 0.056 0.992 6.5 17 73626
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 1.5 1.53 95.2 1.974 2.093 0.679 0.481 9.1
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 1.5 55.6 69924 3613 99.01 0.22845 0.22674 0.2347 0.26196 0.2683 RANDOM 25.384
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.841 r_dihedral_angle_4_deg 15.215 r_dihedral_angle_3_deg 13.26 r_long_range_B_refined 6.043 r_long_range_B_other 5.81 r_dihedral_angle_1_deg 5.474 r_scangle_other 3.753 r_mcangle_it 2.798 r_mcangle_other 2.796 r_angle_other_deg 2.439
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.841 r_dihedral_angle_4_deg 15.215 r_dihedral_angle_3_deg 13.26 r_long_range_B_refined 6.043 r_long_range_B_other 5.81 r_dihedral_angle_1_deg 5.474 r_scangle_other 3.753 r_mcangle_it 2.798 r_mcangle_other 2.796 r_angle_other_deg 2.439 r_scbond_it 2.413 r_scbond_other 2.412 r_mcbond_it 1.889 r_mcbond_other 1.886 r_angle_refined_deg 1.45 r_chiral_restr 0.071 r_bond_other_d 0.035 r_bond_refined_d 0.009 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 3304 Nucleic Acid Atoms Solvent Atoms 558 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement xia2 data scaling MOLREP phasing XDS data reduction