6FEA
A. vinelandii vanadium nitrogenase, turnover state
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 5N6Y | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 295 | 10-13 % PEG 8000 15-20 % ethylene glycol 0.03 M MgCl2 0.1 mM ZnCl2 5 mM Na2S2O4 0.1 M HEPES/NaOH |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.48 | 50.35 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 75.61 | α = 84.05 |
| b = 79.75 | β = 72.44 |
| c = 107.16 | γ = 75.25 |
| Symmetry | |
|---|---|
| Space Group | P 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 | PIXEL | DECTRIS EIGER X 16M | 2017-06-20 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.0000 | SLS | X06SA |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | 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 | 1.2 | 102.12 | 99.6 | 0.115 | 0.072 | 0.998 | 10.1 | 6.5 | 683222 | 2 | 2 | ||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
| 1 | 1.2 | 1.23 | 99.1 | 0.901 | 0.686 | 0.338 | 4.3 | ||||||||||||
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 | 5N6Y | 1.2 | 102.12 | 683222 | 35693 | 99.61 | 0.11827 | 0.11689 | 0.14458 | RANDOM | 15.731 | ||||||
| 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] | |
| 0.14 | 0.07 | 0.25 | 0.29 | -0.15 | -0.22 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.503 |
| r_sphericity_free | 22.921 |
| r_dihedral_angle_4_deg | 18.723 |
| r_rigid_bond_restr | 13.51 |
| r_dihedral_angle_3_deg | 12.555 |
| r_sphericity_bonded | 8.954 |
| r_dihedral_angle_1_deg | 6.257 |
| r_scbond_other | 3.958 |
| r_scbond_it | 3.957 |
| r_long_range_B_refined | 3.824 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 16520 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 2652 |
| Heterogen Atoms | 108 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| SCALA | data scaling |
| MOLREP | phasing |
