3E39
Crystal structure of a putative nitroreductase in complex with fmn (dde_0787) from desulfovibrio desulfuricans subsp. at 1.70 A resolution
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 4.5 | 277 | 40.0000% PEG-400, 0.1M Acetate pH 4.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.07 | 40.46 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 47.78 | α = 90 |
| b = 67.99 | β = 90 |
| c = 99.74 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
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 | Vertical focusing mirror | 2008-07-22 | M | MAD | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRL BEAMLINE BL9-1 | 0.918370,0.979421,0.979155 | SSRL | BL9-1 |
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 | 1.7 | 28.094 | 96.9 | 0.078 | 8.85 | 36111 | -3 | 13.566 | |||||||||||
| 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) | |||||||||||
| 1.7 | 1.76 | 99 | 0.461 | 1.8 | |||||||||||||||
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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
| X-RAY DIFFRACTION | MAD | THROUGHOUT | 1.7 | 28.094 | 36077 | 1806 | 98.96 | 0.166 | 0.165 | 0.201 | RANDOM | 10.969 | |||||||
| 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] | |
| 0.59 | 0.34 | -0.94 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 30.633 |
| r_dihedral_angle_3_deg | 10.441 |
| r_dihedral_angle_4_deg | 10.254 |
| r_scangle_it | 5.229 |
| r_dihedral_angle_1_deg | 4.117 |
| r_scbond_it | 3.766 |
| r_mcangle_it | 2.44 |
| r_mcbond_it | 1.856 |
| r_angle_refined_deg | 1.524 |
| r_angle_other_deg | 0.983 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2664 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 373 |
| Heterogen Atoms | 84 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| PHENIX | refinement |
| SHELX | phasing |
| MolProbity | model building |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| SHELXD | phasing |
| autoSHARP | phasing |
