6RQ7
Gadolinium MRI contrast compound binding in human plasma glycoprotein afamin - resurrection of highly anisotropic data
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| 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 | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.05 | 40 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 103.352 | α = 90 |
| b = 109.734 | β = 90 |
| c = 48.381 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | |
|---|---|
| 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 | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3866 |
| Nucleic Acid Atoms | |
| Solvent Atoms | |
| Heterogen Atoms | 143 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| pointless | data scaling |
| Aimless | data scaling |
| autoPROC | data collection |
| STARANISO | data scaling |
| PHASER | phasing |
