7W5D
High resolution structure of lectin-ike Ox-LDL Receptor 1
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293.15 | protein 8mg/ml, 10mM Tris-HCl, 150mM NaCl, 1.1 M Sodium Malonate, 0.1M HEPES pH 7, 0.5% v/v Jeffamine ED-2001 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.21 | 44.24 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 71.033 | α = 90 |
| b = 49.726 | β = 98.57 |
| c = 76.58 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 1 2 1 |
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 PILATUS 6M-F | 2017-07-16 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 0.984 | ESRF | ID29 |
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 | 1.01 | 75.724 | 91.2 | 0.037 | 0.045 | 0.025 | 0.999 | 12 | 2.9 | 105602 | 12.03 | ||||||||
| 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 | 1.01 | 1.095 | 59.8 | 0.601 | 0.732 | 0.411 | 0.627 | 2.9 | |||||||||||
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 | 1YPQ | 1.141 | 16.62 | 93536 | 4681 | 97.6 | 0.1809 | 0.1802 | 0.1931 | RANDOM | 17.33 | ||||||
| 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] | |
| 0.5836 | 0.8317 | -1.0539 | 0.4703 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| t_other_torsion | 14.94 |
| t_omega_torsion | 4.84 |
| t_angle_deg | 0.99 |
| t_bond_d | 0.009 |
| t_dihedral_angle_d | |
| t_trig_c_planes | |
| t_gen_planes | |
| t_it | |
| t_nbd | |
| t_improper_torsion | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2121 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 369 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| BUSTER | refinement |
| autoPROC | data reduction |
| autoPROC | data scaling |
| PHASER | phasing |
| Coot | model building |
