8VFO
Crystal Structure of L117G 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 | 20-28% PEG 4000, 0.1M Sodium Citrate, 0.2M Ammonium Acetate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.99 | 38.22 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 80.588 | α = 90 |
b = 80.588 | β = 90 |
c = 40.123 | 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 | 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 | |||||||||||||||||||
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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 | 1.35 | 40.29 | 99.6 | 0.049 | 0.056 | 0.025 | 0.999 | 20.4 | 4.5 | 21271 |
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 | 1.35 | 1.37 | 94.8 | 0.252 | 0.306 | 0.171 | 0.902 | 2.8 |
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 | 1.35 | 40.29 | 20211 | 1060 | 99.6 | 0.167 | 0.166 | 0.193 | 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 | |
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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 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 856 |
Nucleic Acid Atoms | |
Solvent Atoms | 171 |
Heterogen Atoms | 13 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data scaling |
MOLREP | phasing |
XDS | data reduction |