8VG5

Crystal Structure of V113N Variant of D-Dopachrome Tautomerase (D-DT) Bound with 4CPPC


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29826-32% PEG 4000, 0.1M Sodium Citrate, 0.2M Ammonium Acetate
Crystal Properties
Matthews coefficientSolvent content
2.3347.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.093α = 90
b = 111.093β = 90
c = 66.07γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90PIXELDECTRIS PILATUS3 S 6M2023-04-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.11583ALS8.3.1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.555.699.10.2330.2390.0560.9926.51773626
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)RedundancyNumber Unique Reflections (All)
11.51.5395.21.9742.0930.6790.4819.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.555.669924361399.010.228450.226740.26196RANDOM25.384
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.841
r_dihedral_angle_4_deg15.215
r_dihedral_angle_3_deg13.26
r_long_range_B_refined6.043
r_long_range_B_other5.81
r_dihedral_angle_1_deg5.474
r_scangle_other3.753
r_mcangle_it2.798
r_mcangle_other2.796
r_angle_other_deg2.439
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.841
r_dihedral_angle_4_deg15.215
r_dihedral_angle_3_deg13.26
r_long_range_B_refined6.043
r_long_range_B_other5.81
r_dihedral_angle_1_deg5.474
r_scangle_other3.753
r_mcangle_it2.798
r_mcangle_other2.796
r_angle_other_deg2.439
r_scbond_it2.413
r_scbond_other2.412
r_mcbond_it1.889
r_mcbond_other1.886
r_angle_refined_deg1.45
r_chiral_restr0.071
r_bond_other_d0.035
r_bond_refined_d0.009
r_gen_planes_other0.007
r_gen_planes_refined0.006
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 AtomsNumber
Protein Atoms3304
Nucleic Acid Atoms
Solvent Atoms558
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
xia2data scaling
MOLREPphasing
XDSdata reduction