2UYK
Crystal structure of E. coli TdcF with bound serine
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1QU9 | PDB ENTRY 1QU9 |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 7 | 10% PEG 1000, 8% PEG 8000, NO BUFFER, pH 7.00 | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.02 | 46.99 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 72.685 | α = 90 |
| b = 86.351 | β = 90 |
| c = 62.598 | 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 | 2003-09-28 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | ESRF | ID14-4 | |
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 | 1.6 | 35.53 | 95.2 | 0.07 | 15.82 | 2.9 | 50532 | 15.8 | |||||||||||
| 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 | 1.6 | 1.63 | 66.4 | 0.12 | 3.02 | ||||||||||||||
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 1QU9 | 1.6 | 35.58 | 50446 | 2598 | 95.7 | 0.157 | 0.155 | 0.199 | RANDOM | 11.32 | ||||||
| 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] | |
| -0.437 | 0.316 | 0.121 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.154 |
| r_dihedral_angle_4_deg | 18.827 |
| r_dihedral_angle_3_deg | 12.325 |
| r_dihedral_angle_1_deg | 5.694 |
| r_scangle_it | 4.797 |
| r_scbond_it | 3.513 |
| r_mcangle_it | 2.064 |
| r_mcbond_it | 1.671 |
| r_angle_refined_deg | 1.555 |
| r_symmetry_vdw_refined | 0.248 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2886 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 457 |
| Heterogen Atoms | 7 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| AMoRE | phasing |
