6UBP
Crystal structure of a photochemical intermediate of human indoleamine 2,3-dioxygenase 1 in complex with carbon monoxide and tryptophan
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 10 | 277 | 100 mM sodium thiosulfate, 100 mM CAPS, pH 10.0, 20% w/v PEG8000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.9 | 57.63 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 86.944 | α = 90 |
b = 97.727 | β = 90 |
c = 130.628 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 100 | PIXEL | DECTRIS EIGER X 16M | 2019-05-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS-II BEAMLINE 17-ID-2 | 0.97931 | NSLS-II | 17-ID-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.95 | 29.34 | 99.9 | 0.098 | 1 | 12.2 | 7.6 | 24106 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.95 | 3.13 | 100 | 2.015 | 0.53 | 1.2 | 8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | PDB entry 5WMU | 2.95 | 29.34 | 22893 | 1165 | 99.85 | 0.2175 | 0.2152 | 0.2641 | RANDOM | 102.551 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-1.87 | -3.07 | 4.94 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.747 |
r_dihedral_angle_3_deg | 18.455 |
r_dihedral_angle_4_deg | 14.062 |
r_dihedral_angle_1_deg | 5.813 |
r_angle_refined_deg | 1.229 |
r_angle_other_deg | 1.034 |
r_chiral_restr | 0.041 |
r_gen_planes_refined | 0.003 |
r_gen_planes_other | 0.003 |
r_bond_refined_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5932 |
Nucleic Acid Atoms | |
Solvent Atoms | 63 |
Heterogen Atoms | 120 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |