3OC7
Crystal structure of an enoyl-CoA hydratase from Mycobacterium avium
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 3MYB | PDB entry 3myb |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 289 | 25.9 mg/mL MyavA.01530.a.A1 PW29874 3C cleaved against JCSG+ condition E11, 0.16 M calcium acetate, 80 mM sodium cacodylate pH 6.5, 14.4% PEG 8000, 20% glycerol, crystal tracking ID 216676e11, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.26 | 45.57 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 83.23 | α = 90 |
b = 83.23 | β = 90 |
c = 93.82 | γ = 120 |
Symmetry | |
---|---|
Space Group | H 3 |
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 315r | 2010-07-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.3 | 0.97946 | ALS | 5.0.3 |
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 | 1.5 | 50 | 100 | 0.066 | 15.9 | 5.4 | 38839 | 38836 | -3 | 20.905 |
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 | 1.5 | 1.54 | 100 | 0.498 | 2.7 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 3myb | 1.5 | 41.62 | 38839 | 38834 | 2020 | 99.9 | 0.1722 | 0.1717 | 0.1808 | RANDOM | 17.6087 |
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] | |
1.02 | 1.02 | -2.05 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.728 |
r_dihedral_angle_4_deg | 14.377 |
r_dihedral_angle_3_deg | 11.051 |
r_dihedral_angle_1_deg | 5.082 |
r_scangle_it | 3.268 |
r_scbond_it | 2.085 |
r_angle_refined_deg | 1.317 |
r_mcangle_it | 1.144 |
r_mcbond_it | 0.629 |
r_chiral_restr | 0.089 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1833 |
Nucleic Acid Atoms | |
Solvent Atoms | 228 |
Heterogen Atoms | 4 |
Software
Software | |
---|---|
Software Name | Purpose |
XSCALE | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |