1YLU
The structure of E. coli nitroreductase with bound acetate, crystal form 2
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1ICV | pdb entry 1ICV |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 291 | PEG4000, ethylene glycol, nicotinic acid, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2 | 36.8 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 155.661 | ¦Á = 90 |
| b = 46.94 | ¦Â = 90 |
| c = 53.658 | ¦Ã = 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 QUANTUM 4 | 2000-11-11 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE BM14 | 0.97626 | ESRF | BM14 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 26.93 | 95.6 | 0.071 | 13.1 | 3 | 26207 | 26207 | 1 | 1 | 15.9 | ||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 2 | 2.11 | 95.7 | 0.173 | 5.4 | 2.6 | 3743 | |||||||||||||
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 1ICV | 2 | 53.45 | 24904 | 1302 | 95.53 | 0.1467 | 0.14384 | 0.20312 | RANDOM | 10.381 | ||||||
| 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] | |
| -0.84 | 2 | -1.16 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_1_deg | 5.498 |
| r_scangle_it | 2.376 |
| r_scbond_it | 1.428 |
| r_angle_refined_deg | 1.077 |
| r_mcangle_it | 0.784 |
| r_angle_other_deg | 0.752 |
| r_mcbond_it | 0.409 |
| r_nbd_other | 0.236 |
| r_symmetry_vdw_other | 0.21 |
| r_symmetry_hbond_refined | 0.204 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3354 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 528 |
| Heterogen Atoms | 72 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MOSFLM | data reduction |
| CCP4 | data scaling |
| CNS | phasing |
