6RQ7
Gadolinium MRI contrast compound binding in human plasma glycoprotein afamin - resurrection of highly anisotropic data
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ESRF BEAMLINE MASSIF-1 |
Synchrotron site | ESRF |
Beamline | MASSIF-1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2018-05-15 |
Detector | DECTRIS PILATUS3 2M |
Wavelength(s) | 0.96598 |
Spacegroup name | P 21 21 2 |
Unit cell lengths | 103.352, 109.734, 48.381 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 75.240 - 2.690 |
R-factor | 0.26629 |
Rwork | 0.263 |
R-free | 0.33544 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5OKL_B |
RMSD bond length | 0.002 |
RMSD bond angle | 1.191 |
Data reduction software | XDS |
Data scaling software | pointless |
Phasing software | PHASER |
Refinement software | REFMAC (5.8.0238) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 75.240 | 3.020 |
High resolution limit [Å] | 2.690 | 2.700 |
Rmerge | 0.180 | 0.540 |
Rmeas | 0.200 | 0.680 |
Number of reflections | 9591 | 486 |
<I/σ(I)> | 5.6 | 1.7 |
Completeness [%] | 85.2 | 62 |
Redundancy | 4.7 | 2.1 |
CC(1/2) | 0.990 | 0.800 |
Crystallization Conditions
crystal 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 |