3BS0
Crystal structure of the P. putida toluene transporter TodX
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 3BRZ | PDB entry 3BRZ |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 295 | 25% PEG 4000, 0.2 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.34 | 47.41 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 38.098 | α = 98.39 |
b = 41.415 | β = 90.01 |
c = 141.064 | γ = 90.06 |
Symmetry | |
---|---|
Space Group | P 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 | ADSC QUANTUM 315 | 2005-02-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | 1.1 | NSLS | X29A |
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 | 46.52 | 100 | 0.074 | 18.3 | 2.8 | 26096 | 26096 | 3 | 53.6 |
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) | |||||||||||
2.5 | 2.59 | 71.2 | 0.274 | 3 | 2.5 | 2115 |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 3BRZ | 2.6 | 11.98 | 25967 | 23644 | 1189 | 91.1 | 0.253 | 0.253 | 0.253 | 0.24 | 0.291 | 0.28 | RANDOM | 52.51 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | ||
10.8 | 2.14 | 7.13 | 10.42 | -17.93 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
x_angle_deg | 1.9 |
x_bond_d | 0.01 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 6238 |
Nucleic Acid Atoms | |
Solvent Atoms | 88 |
Heterogen Atoms | 84 |
Software
Software | |
---|---|
Software Name | Purpose |
PHASER | phasing |
CNS | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |