4FOX
Crystal Structure of Mtb ThyA in complex with dUMP and Raltitrexed
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 3QJ7 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.4 | 298 | 2M ammonium sulfate, 0.1M imidazole 6.4, 5mM spermine, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.53 | 51.34 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 91.342 | α = 90 |
b = 138.444 | β = 107 |
c = 99.948 | 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 | CCD | MARMOSAIC 300 mm CCD | mirrors | 2010-02-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 0.91924 | APS | 23-ID-B |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.3 | 69.22 | 97.8 | 0.112 | 0.112 | 7.6 | 4.05 | 102988 | 102988 | 48.43 |
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 | 2.3 | 2.38 | 96.5 | 0.363 | 2.8 | 4.09 | 10135 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3QJ7 | 2.3 | 45.0089 | 102895 | 102895 | 5139 | 97.7 | 0.2149 | 0.2149 | 0.2126 | 0.2577 | random | 57.2676 |
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] | |
5.237 | 2.115 | -0.832 | -4.405 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 11.29 |
f_nbd_refined | 4.08 |
f_angle_d | 0.767 |
f_chiral_restr | 0.056 |
f_bond_d | 0.006 |
f_plane_restr | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 16473 |
Nucleic Acid Atoms | |
Solvent Atoms | 352 |
Heterogen Atoms | 416 |
Software
Software | |
---|---|
Software Name | Purpose |
d*TREK | data scaling |
d*TREK | data reduction |
PHASER | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |