7X6F
Outer membrane lipoprotein QseG of Escherichia coli O157:H7
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.08 M magnesium acetate tetrahydrate, 0.1 M sodium citrate pH 6.0, 14% (w/v) polyethylene glycol monomethyl ether 5000 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.31 | 46.78 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 42.963 | α = 90 |
b = 149.785 | β = 94.649 |
c = 88.302 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 1 21 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 16M | 2021-12-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL44XU | 0.9000 | SPring-8 | BL44XU |
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 | 2.3 | 43.43 | 98.9 | 0.091 | 0.108 | 0.058 | 0.996 | 8.5 | 3.4 | 48807 |
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 | 2.3 | 2.38 | 99.7 | 0.834 | 0.983 | 0.516 | 0.65 | 1.6 | 3.6 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | AlphaFold structure | 2.3 | 39.803 | 48774 | 2466 | 98.839 | 0.223 | 0.2206 | 0.2735 | 52.887 |
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] | |
-0.095 | -0.031 | -0.006 | 0.105 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.122 |
r_dihedral_angle_3_deg | 21.163 |
r_dihedral_angle_4_deg | 20.35 |
r_lrange_it | 9.305 |
r_scangle_it | 9.106 |
r_scbond_it | 7.534 |
r_mcangle_it | 6.625 |
r_mcbond_it | 5.606 |
r_dihedral_angle_1_deg | 5.332 |
r_angle_refined_deg | 1.513 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 7281 |
Nucleic Acid Atoms | |
Solvent Atoms | 279 |
Heterogen Atoms | 57 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
PHENIX | refinement |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |