1OFN
Purification, crystallisation and preliminary structural studies of dTDP-4-keto-6-deoxy-glucose-5-epimerase (EvaD) from Amycolatopsis orientalis; the fourth enzyme in the dTDP-L-epivancosamine biosynthetic pathway.
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 8 | 25%PEG4K, 100MM MGCL2, 100MM TRIS-HCL, PH8.0, SITTING DROP,, pH 8.00 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.3 | 46.2 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 98.575 | α = 90 |
| b = 71.996 | β = 90 |
| c = 57.1 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 2 |
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 CCD | TOROIDAL MIRROR | 2001-11-15 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-2 | ESRF | ID14-2 | |
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 | 1.5 | 57.735 | 100 | 0.056 | 7.3 | 4.5 | 65259 | ||||||||||||
| 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 | 1.55 | 100 | 0.263 | 2.6 | 4.1 | |||||||||||||
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 | PDB ENTRY 1DZR | 1.5 | 57.74 | 62417 | 3334 | 100 | 0.146 | 0.144 | 0.178 | RANDOM | 12.21 | ||||||
| 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] | |
| -0.49 | 0.62 | -0.13 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_3_deg | 16.943 |
| r_dihedral_angle_1_deg | 5.337 |
| r_scangle_it | 4.947 |
| r_scbond_it | 3.243 |
| r_mcangle_it | 2.231 |
| r_angle_refined_deg | 1.71 |
| r_mcbond_it | 1.446 |
| r_angle_other_deg | 0.754 |
| r_symmetry_vdw_refined | 0.44 |
| r_symmetry_hbond_refined | 0.402 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3123 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 543 |
| Heterogen Atoms | 24 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALEPACK | data scaling |
| AMoRE | phasing |
