3PET
Crystal structure of a putative adhesin (BF0245) from Bacteroides fragilis NCTC 9343 at 2.07 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 3.85 | 293 | 0.20M sodium chloride, 31.8% polyethylene glycol 300, 0.1M sodium acetate pH 3.85, NANODROP, temperature 293K, VAPOR DIFFUSION, SITTING DROP |
2 | VAPOR DIFFUSION, SITTING DROP | 4.5 | 277 | GNF2 E12: 0.20M sodium chloride, 40.0% polyethylene glycol 300, 0.1M sodium acetate pH 4.5, NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 38.59 | α = 90 |
b = 60.7 | β = 90 |
c = 205.11 | 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 | CCD | MARMOSAIC 325 mm CCD | 2010-07-22 | M | MAD | ||||||
2 | 2 | x-ray | 100 | CCD | MARMOSAIC 325 mm CCD | 2010-04-08 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | SSRL | BL9-2 | |
2 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.97954, 0.91837, 0.97917 | SSRL | BL11-1 |
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 | ||||||||
1,2 | 2.07 | 45.392 | 100 | 0.153 | 8.85 | 30470 | -3 | 21.558 |
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) | |||||||||||
1,2 | 2.07 | 2.14 | 100 | 0.814 | 2.2 |
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 | MAD | THROUGHOUT | 2.07 | 45.392 | 30217 | 1530 | 0.1775 | 0.1758 | 0.2102 | RANDOM | 28.836 |
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] | |
-5.6207 | -0.9225 | 6.5433 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
t_omega_torsion | 3.83 |
t_other_torsion | 2.71 |
t_angle_deg | 1.22 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_trig_c_planes | |
t_gen_planes | |
t_it | |
t_nbd | |
t_improper_torsion |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3204 |
Nucleic Acid Atoms | |
Solvent Atoms | 304 |
Heterogen Atoms | 151 |
Software
Software | |
---|---|
Software Name | Purpose |
XSCALE | data processing |
SHELX | phasing |
SHARP | phasing |
BUSTER-TNT | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
XSCALE | data scaling |
SHELXD | phasing |
autoSHARP | phasing |
BUSTER | refinement |