8OFD
Crystal structure of beta-conglutin from Lupinus albus refined to 2.81 A
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1UIJ |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 281 | 40% (v/v) Tacsimate pH 7.0, 50 mM HEPES pH 7.0, 2 mM Spermine, and 2 mM Hexaamine cobalt (III) |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.38 | 63.68 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 166.63 | α = 90 |
b = 166.63 | β = 90 |
c = 40.098 | 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 | RIGAKU HyPix-6000HE | 2022-04-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SEALED TUBE | RIGAKU PhotonJet-S | 1.54184 |
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 | 2.81 | 21.77 | 99.7 | 0.17 | 0.182 | 0.064 | 0.993 | 9.1 | 7.8 | 15700 | 55 |
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 | 2.81 | 2.96 | 100 | 1.001 | 1.067 | 0.366 | 0.657 | 2 | 8.4 |
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 | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.81 | 21.767 | 15686 | 774 | 99.771 | 0.208 | 0.204 | 0.2772 | 62.202 |
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] | |
0.895 | 0.895 | -1.79 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 20.804 |
r_dihedral_angle_6_deg | 14.932 |
r_lrange_other | 12.243 |
r_lrange_it | 12.238 |
r_dihedral_angle_2_deg | 11.377 |
r_dihedral_angle_1_deg | 8.748 |
r_scangle_it | 7.904 |
r_scangle_other | 7.903 |
r_mcangle_it | 7.673 |
r_mcangle_other | 7.672 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3281 |
Nucleic Acid Atoms | |
Solvent Atoms | 82 |
Heterogen Atoms | 6 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
CrysalisPro | data reduction |
Aimless | data scaling |
MOLREP | phasing |