4GZ9
Mouse Neuropilin-1, extracellular domains 1-4 (a1a2b1b2)
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | 0.1M HEPES, pH 7.5, 1.5M lithium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 245.359 | α = 90 |
| b = 245.359 | β = 90 |
| c = 47.93 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 3 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 2M | 2011-04-14 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.9173 | Diamond | I04-1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 2.7 | 81 | 99.4 | 45127 | 45127 | -3 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2QQM, 2QQK | 2.7 | 81 | -3 | 45078 | 42837 | 2241 | 99.18 | 0.20007 | 0.20007 | 0.19889 | 0.22279 | RANDOM | 68.168 | |||
| 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] | |
| 1.61 | 0.81 | 1.61 | -2.42 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.049 |
| r_dihedral_angle_4_deg | 17.694 |
| r_dihedral_angle_3_deg | 16.835 |
| r_dihedral_angle_1_deg | 7.096 |
| r_angle_refined_deg | 1.582 |
| r_angle_other_deg | 0.761 |
| r_chiral_restr | 0.083 |
| r_bond_refined_d | 0.009 |
| r_gen_planes_refined | 0.005 |
| r_bond_other_d | 0.001 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4472 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 29 |
| Heterogen Atoms | 77 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| GDA | data collection |
| PHASER | phasing |
| REFMAC | refinement |
| MOSFLM | data reduction |
| Aimless | data scaling |
