8VG7
Crystal Structure of T115A Variant of D-Dopachrome Tautomerase (D-DT)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1DPT |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 298 | 28-30% PEG 4000, 0.1M Sodium Citrate pH 5.8-6.2, 0.2M Ammonium Acetate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.11 | 41.76 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 82.281 | α = 90 |
b = 82.281 | β = 90 |
c = 40.732 | γ = 120 |
Symmetry | |
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Space Group | H 3 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 280 | PIXEL | DECTRIS PILATUS3 S 6M | 2022-08-13 | 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 | |||||||||||||||||||
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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 | 1.24 | 41.14 | 99.8 | 0.07 | 0.079 | 0.035 | 0.996 | 14.2 | 4.7 | 29080 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.24 | 1.26 | 96.5 | 0.269 | 0.334 | 0.195 | 0.875 | 2.6 |
Refinement
Statistics | |||||||||||||||||||
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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 | 1.24 | 41.14 | 27635 | 1443 | 99.76 | 0.10091 | 0.09977 | 0.12343 | RANDOM | 13.128 |
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 | 0.01 | 0.01 | -0.03 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 27.5 |
r_dihedral_angle_4_deg | 17.181 |
r_dihedral_angle_3_deg | 11.118 |
r_dihedral_angle_1_deg | 5.929 |
r_rigid_bond_restr | 5.313 |
r_scangle_other | 3.563 |
r_long_range_B_refined | 3.187 |
r_long_range_B_other | 3.043 |
r_scbond_it | 2.888 |
r_scbond_other | 2.888 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 883 |
Nucleic Acid Atoms | |
Solvent Atoms | 99 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data scaling |
MOLREP | phasing |
XDS | data reduction |