6RLO
Crystal structure of AT1412dm Fab fragment in complex with CD9 large extracellular loop
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6RLM | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 6.2 | 293.15 | PEG 1000, sodium chloride, sodium potassium phosphate |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.58 | 52.24 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 73.776 | α = 71.12 |
| b = 89.858 | β = 89.59 |
| c = 91.533 | γ = 85.96 |
| Symmetry | |
|---|---|
| Space Group | P 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 EIGER X 4M | 2017-12-01 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE MASSIF-3 | 0.96 | ESRF | MASSIF-3 |
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 | 2.2 | 84.8 | 92.6 | 0.199 | 0.231 | 0.117 | 0.984 | 5 | 3.9 | 104319 | |||||||||
| 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 | 2.2 | 2.24 | 94.6 | 1.048 | 1.216 | 0.615 | 0.982 | 3.9 | |||||||||||
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 | 6RLM | 2.2 | 84.8 | 98939 | 5338 | 92.6 | 0.2553 | 0.2537 | 0.2866 | RANDOM | 29.944 | ||||||
| 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] | |
| -2.62 | -0.09 | 0.84 | 2.94 | -1.19 | -0.98 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 35.664 |
| r_dihedral_angle_4_deg | 22.121 |
| r_dihedral_angle_3_deg | 17.439 |
| r_dihedral_angle_1_deg | 7.87 |
| r_angle_refined_deg | 1.34 |
| r_angle_other_deg | 1.145 |
| r_chiral_restr | 0.05 |
| r_gen_planes_refined | 0.005 |
| r_bond_refined_d | 0.004 |
| r_bond_other_d | 0.001 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 15644 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 212 |
| Heterogen Atoms | 19 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| DIALS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
| Coot | model building |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
