5EFI
Crystal structure of mouse CD1d in complex with the p99p lipopeptide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 3G08 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | ammonium citrate, PEG4000 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.67 | 53.86 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 42.19 | α = 90 |
b = 107.85 | β = 90 |
c = 110.34 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 21 21 |
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 | PSI PILATUS 6M | 2014-01-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.9794 | SSRL | BL11-1 |
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 | 1.8 | 49.12 | 97.4 | 10.9 | 3.5 | 46178 |
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 | 3G08 | 1.8 | 49.12 | 43789 | 2345 | 96.89 | 0.21988 | 0.21857 | 0.24387 | RANDOM | 34.966 |
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 | 0.2 | 1.41 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.069 |
r_dihedral_angle_4_deg | 16.734 |
r_dihedral_angle_3_deg | 12.12 |
r_dihedral_angle_1_deg | 6.448 |
r_long_range_B_refined | 5.149 |
r_long_range_B_other | 5.149 |
r_angle_refined_deg | 1.334 |
r_angle_other_deg | 0.847 |
r_mcangle_it | 0.758 |
r_mcangle_other | 0.758 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2980 |
Nucleic Acid Atoms | |
Solvent Atoms | 204 |
Heterogen Atoms | 154 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
Coot | model building |