8TT9
X-ray structure of Macrophage Migration Inhibitory Factor (MIF) Covalently Bound to 4-hydroxyphenylpyruvate (HPP)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3IJJ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | 2M AMMONIUM SULFATE, 4% ISOPROPANOL, 0.1 M TRIS(HYDROXYMETHYL)AMINOMETHAN; MIXED WITH PROTEIN:INHIBITOR COMPLEX IN A 1:10 RATIO |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.82 | 56.33 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68.57 | α = 90 |
b = 68.87 | β = 90 |
c = 88.43 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 293 | CMOS | RDI CMOS_8M | 2018-05-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 4.2.2 | 1.0 | ALS | 4.2.2 |
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 | 1.68 | 44.22 | 100 | 0.076 | 0.085 | 0.04 | 0.998 | 16.1 | 7.6 | 48464 | 28.05 |
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 | 1.68 | 1.71 | 100 | 2.208 | 2.426 | 1.302 | 0.314 | 6.4 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.68 | 44.22 | 0.31 | 48298 | 2346 | 99.73 | 0.1717 | 0.1703 | 0.1992 | 33.87 |
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 |
f_dihedral_angle_d | 15.6625 |
f_angle_d | 1.3355 |
f_chiral_restr | 0.092 |
f_bond_d | 0.0144 |
f_plane_restr | 0.0096 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2563 |
Nucleic Acid Atoms | |
Solvent Atoms | 174 |
Heterogen Atoms | 47 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |
pointless | data scaling |
PHASER | phasing |