3OME
Crystal structure of a probable ENOYL-COA Hydratase from Mycobacterium Smegmatis
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 3H8L | PDB entry 3h8l |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 290 | EBS JCSG+ SCEEN E11: 160MM CAOAC2, 80MM CACODYLATE PH 6.5, 14.4% PEG 8000, 20% GLYCEROL, MYSMA.00358.E.A1 PS00544 AT 30MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.53 | 51 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 145.22 | α = 90 |
b = 86.65 | β = 97.93 |
c = 140.05 | γ = 90 |
Symmetry | |
---|---|
Space Group | C 1 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 | CCD | ADSC QUANTUM 315r | 2009-07-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.2 | 1.000 | ALS | 5.0.2 |
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 | 2.05 | 50 | 99.9 | 0.079 | 11.89 | 4.5 | 108008 | 107914 | -3 | 35.58 |
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 | 2.05 | 2.1 | 99.8 | 0.497 | 2.7 | 4.4 | 7953 |
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 | PDB entry 3h8l | 2.05 | 50 | 108008 | 107778 | 5373 | 99.8 | 0.147 | 0.147 | 0.145 | 0.174 | RANDOM | 35.03 |
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] | |
0.11 | -0.47 | 1.23 | -1.47 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.108 |
r_dihedral_angle_4_deg | 16.15 |
r_dihedral_angle_3_deg | 12.559 |
r_dihedral_angle_1_deg | 5.432 |
r_scangle_it | 3.738 |
r_scbond_it | 2.296 |
r_mcangle_it | 1.345 |
r_angle_refined_deg | 1.34 |
r_angle_other_deg | 0.93 |
r_mcbond_it | 0.726 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 11189 |
Nucleic Acid Atoms | |
Solvent Atoms | 666 |
Heterogen Atoms | 6 |
Software
Software | |
---|---|
Software Name | Purpose |
BOS | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |