5EIZ
Crystal structure of Y99A mutant of human macrophage migration inhibitory factor
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3DJH | PDB ENTRY 3DJH |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | 2 M ammonium sulfate, 3% 2-propanol, 0.1 M Tris-HCl, pH 7.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.7 | 54.53 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 67.696 | α = 90 |
b = 67.958 | β = 90 |
c = 86.519 | 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 PILATUS 200K | 2015-04-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.5418 |
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) | 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 | 1.96 | 50 | 99.1 | 0.039 | 0.045 | 0.021 | 24.6 | 4.2 | 28977 |
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 | 1.96 | 1.99 | 94.8 | 0.059 | 0.07 | 0.036 | 0.993 | 3.3 | 1367 |
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 3DJH | 1.96 | 47.96 | 27443 | 1486 | 98.98 | 0.1579 | 0.1566 | 0.1811 | RANDOM | 17.733 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 42.7 |
r_dihedral_angle_4_deg | 20.212 |
r_dihedral_angle_3_deg | 11.026 |
r_dihedral_angle_1_deg | 4.994 |
r_angle_other_deg | 3.757 |
r_angle_refined_deg | 1.82 |
r_mcangle_it | 1.777 |
r_mcbond_it | 1.366 |
r_mcbond_other | 1.358 |
r_chiral_restr | 0.122 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2530 |
Nucleic Acid Atoms | |
Solvent Atoms | 311 |
Heterogen Atoms | 41 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
HKL-2000 | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
DENZO | data reduction |
PHASER | phasing |