Crystal structure of a putative nitroreductase (tm1586) from thermotoga maritima msb8 at 2.00 A resolution
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION,SITTING DROP,NANODROP | 4.6 | 277 | Acetate pH 4.6, 0.2M (NH4)2SO4, 20% Glycerol, 25% PEG-4000 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.2 | 43.58 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 45.299 | α = 90 |
| b = 45.299 | β = 90 |
| c = 192.752 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 31 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 315 | 2004-04-04 | M | SINGLE WAVELENGTH | ||||||
| 2 | 1 | x-ray | M | MAD | ||||||||||
| 1,2 | 1 | |||||||||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | SSRL | BL9-2 | |
| 2 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.979029, 0.918370,0.978835 | SSRL | BL9-2 |
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 | 2 | 39.23 | 97.1 | 0.059 | 18 | 5.7 | 15922 | 41.38 | |||||||||||
| 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) | |||||||||||
| 1,2 | 2 | 2.05 | 82.3 | 0.229 | 3.2 | 3.2 | 969 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MAD | THROUGHOUT | 2 | 39.23 | 15544 | 827 | 99.79 | 0.2118 | 0.21022 | 0.22 | 0.24281 | 0.25 | RANDOM | 32.938 | |||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
| 0.29 | 0.15 | 0.29 | -0.44 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 31.558 |
| r_dihedral_angle_3_deg | 14.704 |
| r_dihedral_angle_4_deg | 9.222 |
| r_dihedral_angle_1_deg | 5.944 |
| r_scangle_it | 4.967 |
| r_scbond_it | 3.796 |
| r_mcangle_it | 2.219 |
| r_mcbond_it | 1.529 |
| r_angle_refined_deg | 1.13 |
| r_angle_other_deg | 0.739 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1751 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 95 |
| Heterogen Atoms | 10 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| MOSFLM | data reduction |
| SCALA | data scaling |
| SOLVE | phasing |
| SHARP | phasing |
| REFMAC | refinement |
| CCP4 | data scaling |
