8VFN
Crystal Structure of WT D-Dopachrome Tautomerase (D-DT) at 310K
X-RAY DIFFRACTION
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 | 44.82 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 84.292 | α = 90 |
b = 84.292 | β = 90 |
c = 41.058 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 3 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 310 | 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 | 1.29 | 73 | 97.9 | 0.091 | 0.096 | 0.031 | 0.999 | 11.4 | 9.1 | 80478 |
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 | 1.29 | 1.31 | 78.8 | 1.423 | 1.618 | 0.747 | 0.329 | 4.5 |
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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.29 | 73 | 76386 | 4085 | 97.93 | 0.15976 | 0.15934 | 0.16735 | RANDOM | 16.598 |
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 | 29.269 |
r_dihedral_angle_4_deg | 15.471 |
r_dihedral_angle_3_deg | 12.199 |
r_rigid_bond_restr | 6.785 |
r_dihedral_angle_1_deg | 6.382 |
r_angle_other_deg | 2.429 |
r_angle_refined_deg | 1.682 |
r_chiral_restr | 0.091 |
r_bond_other_d | 0.035 |
r_bond_refined_d | 0.013 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2655 |
Nucleic Acid Atoms | |
Solvent Atoms | 234 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
xia2 | data scaling |
PHASER | phasing |
XDS | data reduction |