3GM6
Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in complex with phosphate
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2OT4 | PDB ENTRY 2OT4 |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 278 | Protein solution (2.5mcl): 9.3mg/ml TvNiR, 0.1M potassium phosphate (pH7.0). Reservoir solution (2.5mcl): 0.2M ammonium acetate, 0.1M tri-sodium citrate dihydrate, 30% v/v 2-methyl-2,4-pentanediol (pH6.5), VAPOR DIFFUSION, HANGING DROP, temperature 278.0K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 4.49 | 72.38 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 196.56 | α = 90 |
| b = 196.56 | β = 90 |
| c = 196.56 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 3 |
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 | MAR CCD 165 mm | 2007-05-30 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | KURCHATOV SNC BEAMLINE K4.4 | 0.998 | KURCHATOV SNC | K4.4 |
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 | 1.8 | 19.9 | 97.8 | 0.096 | 10 | 226620 | |||||||||||||
| 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) | |||||||||||
| 1.79 | 1.85 | 99.8 | 0.229 | 4.9 | |||||||||||||||
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 2OT4 | 1.8 | 19.9 | 215207 | 11413 | 97.7 | 0.1593 | 0.15862 | 0.172 | RANDOM | 18.146 | ||||||
| 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] | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 36.191 |
| r_dihedral_angle_4_deg | 17.434 |
| r_dihedral_angle_3_deg | 12.348 |
| r_dihedral_angle_1_deg | 5.895 |
| r_scangle_it | 2.742 |
| r_scbond_it | 1.932 |
| r_angle_refined_deg | 1.529 |
| r_mcangle_it | 1.2 |
| r_angle_other_deg | 1.006 |
| r_mcbond_it | 0.859 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 8226 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1038 |
| Heterogen Atoms | 732 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| HKL-2000 | data collection |
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
