9D77
Crystal form of Netrin-1 mimics nanotubes
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 7LRF |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | 40% v/v 2-methyl-2,4-pentanediol; 5% w/v polyethylene glycol 8000; 100 mM 2-(N-morpholino)ethanesulfonic acid; pH 6.5 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
4.53 | 72.86 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 189.26 | α = 90 |
b = 189.26 | β = 90 |
c = 45.88 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 6 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | IMAGE PLATE | RIGAKU RAXIS IV++ | Rigaku Osmic Confocal Max-Flux multilayer mirror | 2017-06-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54187 |
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 | 3.4 | 35.77 | 68.9 | 0.412 | 0.435 | 0.14 | 0.994 | 4.9 | 9.6 | 9185 | 83.7 |
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 | 3.4 | 4.2 | 33.53 | 1.473 | 1.553 | 0.488 | 0.583 | 1.9 | 9.8 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3.4 | 35.77 | 9185 | 743 | 68.74 | 0.3 | 0.2967 | 0.3348 | Random selection | 88.104 |
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] | |
-4.198 | -2.099 | -4.198 | 13.618 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 17.949 |
r_dihedral_angle_6_deg | 14.042 |
r_dihedral_angle_1_deg | 10.352 |
r_dihedral_angle_other_1_deg | 8.932 |
r_dihedral_angle_2_deg | 7.406 |
r_lrange_it | 2.853 |
r_lrange_other | 2.853 |
r_angle_refined_deg | 1.847 |
r_scangle_it | 1.532 |
r_scangle_other | 1.532 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3272 |
Nucleic Acid Atoms | |
Solvent Atoms | 20 |
Heterogen Atoms | 225 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data collection |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |
Coot | model building |