3ZIY
Structure of three-domain heme-Cu nitrite reductase from Ralstonia pickettii at 1.01 A resolution
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2Z00 | PDB ENTRY 2Z00 |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 6.5 | PEG, SODIUM CITRITE, pH 6.5 | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.48 | 50 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 128.177 | α = 90 |
| b = 128.177 | β = 90 |
| c = 86.314 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | H 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 | PIXEL | DECTRIS PILATUS 6M | MIRRORS | 2012-10-04 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 1 | SOLEIL | PROXIMA 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 | 1.01 | 40 | 100 | 0.08 | 18 | 4.3 | 277728 | 6.4 | |||||||||||
| 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 | 1.01 | 1.05 | 99.9 | 0.62 | 2 | 3.4 | |||||||||||||
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 2Z00 | 1.01 | 37.76 | 263699 | 14029 | 99.91 | 0.10962 | 0.10898 | 0.12182 | RANDOM | 12.6 | ||||||
| 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] | |
| -0.01 | -0.01 | -0.01 | 0.02 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_sphericity_free | 45.916 |
| r_dihedral_angle_2_deg | 39.116 |
| r_dihedral_angle_4_deg | 20.71 |
| r_dihedral_angle_3_deg | 12.101 |
| r_sphericity_bonded | 9.78 |
| r_dihedral_angle_1_deg | 6.782 |
| r_rigid_bond_restr | 4.678 |
| r_angle_other_deg | 2.207 |
| r_angle_refined_deg | 1.855 |
| r_chiral_restr | 0.117 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3440 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 794 |
| Heterogen Atoms | 45 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| MOLREP | phasing |
