4R8O
Crystal structure of a DUF3836 family protein (BVU_1206) from Bacteroides vulgatus ATCC 8482 at 2.50 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 25.0% Glycerol 1.50M ammonium sulfate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
4.91 | 74.94 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 98.08 | α = 90 |
b = 98.08 | β = 90 |
c = 89.24 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 31 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 | DECTRIS PILATUS 6M | Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) | 2014-06-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 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 | 2.5 | 49.04 | 99.4 | 0.087 | 16.06 | 9.79 | 17436 | -3 | 84.846 |
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 | 2.5 | 2.57 | 98.3 | 2.439 | 0.75 | 8.92 |
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 | 2.5 | 49.04 | 17387 | 881 | 99.13 | 0.18 | 0.1768 | 0.2444 | RANDOM | 79.4772 |
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] | |
-41.18 | -41.18 | 82.36 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.512 |
r_dihedral_angle_4_deg | 15.678 |
r_dihedral_angle_3_deg | 13.753 |
r_mcangle_it | 6.423 |
r_dihedral_angle_1_deg | 6.113 |
r_mcbond_other | 4.182 |
r_mcbond_it | 4.181 |
r_angle_refined_deg | 1.707 |
r_angle_other_deg | 1.464 |
r_chiral_restr | 0.1 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1648 |
Nucleic Acid Atoms | |
Solvent Atoms | 17 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
MolProbity | model building |
PDB_EXTRACT | data extraction |
PHASER | phasing |
XSCALE | data scaling |
REFMAC | refinement |
XDS | data reduction |