5HUD
Non-covalent complex of and DAHP synthase and chorismate mutase from Corynebacterium glutamicum with bound transition state analog
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 2W1A |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | 100 mM imidazole/MES buffer, pH 6.5 30 mM each of ethylene glycol mix (di-ethylene glycol, tri-ethylene glycol, tetra-ethylene glycol, penta-ethylene glycol) 15% glycerol 15% PEG 4000 micro-seeded from badly diffracting crystals (approx. 8 AA resolution), in 100 mM Na-HEPES, pH 7.5, 200 mM LiSO4, 25% PEG 3350 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.45 | 64.31 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 117.622 | α = 90 |
b = 110.481 | β = 101.41 |
c = 134.652 | 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 | PIXEL | DECTRIS PILATUS 6M | 2015-07-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 0.97239 | ESRF | ID29 |
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 | 2.1 | 131.99 | 96.7 | 0.199 | 4.79 | 2.95 | 190339 |
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 | 2.1 | 2.23 | 85.7 | 1.763 | 0.44 | 2.24 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | 2W1A | 2.15 | 40 | 170847 | 8846 | 97.99 | 0.25191 | 0.24952 | 0.298 | RANDOM | 33.789 |
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] | |
0.57 | 0.09 | -1.03 | 0.4 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.924 |
r_dihedral_angle_3_deg | 16.337 |
r_dihedral_angle_4_deg | 16.187 |
r_dihedral_angle_1_deg | 6.091 |
r_long_range_B_refined | 5.8 |
r_long_range_B_other | 5.8 |
r_scangle_other | 3.552 |
r_mcangle_it | 3.154 |
r_mcangle_other | 3.154 |
r_scbond_it | 2.165 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 16558 |
Nucleic Acid Atoms | |
Solvent Atoms | 779 |
Heterogen Atoms | 871 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
PHASER | phasing |
Aimless | data scaling |
XDS | data scaling |
XDS | data reduction |