4O3V
Crystal structure of a VirB8-like protein of type IV secretion system from Rickettsia typhi
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 289 | RityA.18390.a.B2 PS01633 at 11.2 mg/mL against CSHT A2, 0.4 M potassium sodium tartrate, cryo-protected with Al's oil, crystal grew over 7 months, crystal tracking ID 250519a2, unique puck ID zuk7-16, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.42 | 64.04 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 117.68 | α = 90 |
b = 117.68 | β = 90 |
c = 83.82 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 41 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 | ADSC QUANTUM 315r | 2013-12-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.2 | 1.0 | ALS | 5.0.2 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.95 | 50 | 100 | 0.065 | 24.26 | 9.6 | 43393 | -3 | 30.753 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.95 | 2 | 100 | 0.477 | 4.15 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.95 | 50 | 43389 | 2182 | 99.97 | 0.1667 | 0.1656 | 0.1892 | RANDOM | 31.9189 |
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] | |
-1.07 | -1.07 | 2.15 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.052 |
r_dihedral_angle_4_deg | 22.704 |
r_dihedral_angle_3_deg | 12.745 |
r_dihedral_angle_1_deg | 6.865 |
r_mcangle_it | 3.16 |
r_mcbond_it | 2.009 |
r_mcbond_other | 2.006 |
r_angle_refined_deg | 1.464 |
r_angle_other_deg | 0.805 |
r_chiral_restr | 0.099 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2226 |
Nucleic Acid Atoms | |
Solvent Atoms | 318 |
Heterogen Atoms | 10 |
Software
Software | |
---|---|
Software Name | Purpose |
XSCALE | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |