☰ Navigation Tabs
Crystal Structure of WT D-Dopachrome Tautomerase (D-DT) at 290K
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 24-30% PEG 4000, 0.1M Sodium Citrate (pH 5.6-6.0), 0.2M Ammonium Acetate
Crystal Properties Matthews coefficient Solvent content 2.23 44.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.351 α = 90 b = 84.351 β = 90 c = 41.032 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 290 PIXEL DECTRIS PILATUS3 S 6M 2022-06-15 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 1.23 73.05 92.1 0.086 0.097 0.044 0.997 8.1 4.3 87432
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 1.23 1.25 44 0.879 1.201 0.812 0.268 1.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.23 73.05 83207 4224 92.11 0.14503 0.14325 0.17988 0.1858 RANDOM 15.31
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 28.166 r_dihedral_angle_4_deg 17.521 r_rigid_bond_restr 12.028 r_dihedral_angle_3_deg 11.493 r_dihedral_angle_1_deg 5.975 r_scangle_other 3.37 r_long_range_B_refined 3.279 r_long_range_B_other 3.077 r_scbond_it 2.938 r_scbond_other 2.937
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.166 r_dihedral_angle_4_deg 17.521 r_rigid_bond_restr 12.028 r_dihedral_angle_3_deg 11.493 r_dihedral_angle_1_deg 5.975 r_scangle_other 3.37 r_long_range_B_refined 3.279 r_long_range_B_other 3.077 r_scbond_it 2.938 r_scbond_other 2.937 r_angle_other_deg 2.69 r_angle_refined_deg 1.851 r_mcangle_other 1.714 r_mcangle_it 1.712 r_mcbond_it 1.44 r_mcbond_other 1.435 r_chiral_restr 0.115 r_bond_other_d 0.035 r_gen_planes_other 0.016 r_bond_refined_d 0.015 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2652 Nucleic Acid Atoms Solvent Atoms 296 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data scaling PHASER phasing XDS data reduction