6XRS
Crystal structure of a GTP-binding protein EngA (Der homolog) from Neisseria gonorrhoeae bound to GDP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.6 | 287 | NegoA.00852.a.D11.PD38388 CID102204 at 3.75 mg/mL against a focus screen based off Morpheus B10 6% PEG 8000, 20% ethylene glycol, 0.03 M NaF, 0.03 M NaBr, 0.03 M NaI, 0.1 M Bicine pH 8.6, crystal tracking ID 315086f2, unique puck ID loy8-5 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.74 | 59.4 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 138.16 | α = 90 |
b = 139.64 | β = 90 |
c = 127 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | RAYONIX MX-300 | 2020-06-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 2.8 | 46.98 | 99.8 | 0.095 | 0.104 | 0.997 | 12.65 | 6.209 | 61091 | 58.184 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.8 | 2.87 | 100 | 0.648 | 0.707 | 0.901 | 3.26 | 6.301 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 5dn8 | 2.8 | 46.98 | 1.99 | 61026 | 3118 | 99.77 | 0.2047 | 0.203 | 0.2354 | 59.6084 |
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] | |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 11607 |
Nucleic Acid Atoms | |
Solvent Atoms | 108 |
Heterogen Atoms | 233 |
Software
Software | |
---|---|
Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
MOLREP | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |