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Crystal Structure of L117G 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 298 20-28% PEG 4000, 0.1M Sodium Citrate, 0.2M Ammonium Acetate
Crystal Properties Matthews coefficient Solvent content 1.99 38.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.588 α = 90 b = 80.588 β = 90 c = 40.123 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 2023-06-23 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 1.35 40.29 99.6 0.049 0.056 0.025 0.999 20.4 4.5 21271
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 1.35 1.37 94.8 0.252 0.306 0.171 0.902 2.8
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 1.35 40.29 20211 1060 99.6 0.167 0.166 0.1661 0.193 0.1926 RANDOM 9.9
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 28.753 r_dihedral_angle_4_deg 21.103 r_dihedral_angle_3_deg 10.139 r_dihedral_angle_1_deg 6.557 r_long_range_B_refined 3.627 r_long_range_B_other 3.278 r_angle_other_deg 2.48 r_scangle_other 2.442 r_angle_refined_deg 1.801 r_scbond_it 1.691
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.753 r_dihedral_angle_4_deg 21.103 r_dihedral_angle_3_deg 10.139 r_dihedral_angle_1_deg 6.557 r_long_range_B_refined 3.627 r_long_range_B_other 3.278 r_angle_other_deg 2.48 r_scangle_other 2.442 r_angle_refined_deg 1.801 r_scbond_it 1.691 r_scbond_other 1.685 r_mcangle_other 1.226 r_mcangle_it 1.217 r_mcbond_it 0.819 r_mcbond_other 0.787 r_chiral_restr 0.097 r_bond_other_d 0.035 r_gen_planes_other 0.014 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 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 856 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement xia2 data scaling MOLREP phasing XDS data reduction