6RQ7
Gadolinium MRI contrast compound binding in human plasma glycoprotein afamin - resurrection of highly anisotropic data
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5OKL | 5OKL_B |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 293 | Stock: 5 mg/ml AFM in 20mM HEPES pH 7.5, 150mM NaCl, incubated with 10mM Gd-DO3A Drop: 200 nL AFM stock + 200 nL of precipitate in hanging drop vapor diffusion (EMBL HTX) Precipitant: 23 to 28% PEG4k, 0.2M NH4SO4, 0.1 M CH3COONH4, pH 5.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.05 | 40 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 103.352 | α = 90 |
b = 109.734 | β = 90 |
c = 48.381 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 PILATUS3 2M | BE CRL | 2018-05-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE MASSIF-1 | 0.96598 | ESRF | MASSIF-1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 2.69 | 75.24 | 85.2 | 0.18 | 0.2 | 0.99 | 5.6 | 4.7 | 9591 | 59.1 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.7 | 3.02 | 62 | 0.54 | 0.68 | 0.8 | 1.7 | 2.1 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 5OKL_B | 2.69 | 75.24 | 9041 | 482 | 59.59 | 0.26629 | 0.26257 | 0.33544 | RANDOM | 56.545 |
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] | |
-0.61 | -0.67 | 1.28 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.84 |
r_dihedral_angle_3_deg | 18.934 |
r_dihedral_angle_4_deg | 11.986 |
r_long_range_B_refined | 10.57 |
r_long_range_B_other | 10.568 |
r_scangle_other | 7.348 |
r_mcangle_it | 6.902 |
r_mcangle_other | 6.902 |
r_dihedral_angle_1_deg | 5.599 |
r_scbond_it | 4.315 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3866 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 143 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
pointless | data scaling |
Aimless | data scaling |
autoPROC | data collection |
STARANISO | data scaling |
PHASER | phasing |