8Q5V
MgADP-bound Fe protein of the molybdenum nitrogenase from Methanothermococcus thermolithotrophicus
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 8Q50 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 293.15 | The purified protein was crystallised at a final concentration of 32.7 mg/ml with 10 mM ATP and 10 mM MgCl2 by spotting 0.5 ul of crystallisation solution with 0.5 ul of protein sample. Crystallisation was done anaerobically in a Coy tent containing N2/H2 (97:3%) atmosphere. The screening was done at 20 degrees Celsius on 96-Well MRC 2-drop polystyrene (SWISSCI) plates containing 90 ul of crystallisation solution. The crystallisation solution in which crystals were obtained contained 20 % w/v polyethylene glycol 8000, 100 mM Tris pH 8.5 and 200 mM magnesium chloride. The crystals were soaked in the crystallisation solution supplemented with 30% glycerol prior freezing in liquid nitrogen. |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.48 | 50.53 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 61.478 | α = 93.98 |
b = 87.594 | β = 98.58 |
c = 182.048 | γ = 109.65 |
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 PILATUS 2M-F | 2020-01-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06DA | 1.00004 | SLS | X06DA |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 2.74 | 71 | 90.5 | 0.284 | 0.307 | 0.117 | 0.983 | 4.5 | 6.7 | 66142 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.74 | 2.9 | 63.1 | 1.224 | 1.358 | 0.509 | 0.526 | 1.6 | 6.7 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2.74 | 39.93 | 1.96 | 66105 | 3242 | 72.08 | 0.219 | 0.2172 | 0.2543 | 60.62 |
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 |
f_dihedral_angle_d | 15.84 |
f_angle_d | 1.239 |
f_chiral_restr | 0.085 |
f_bond_d | 0.009 |
f_plane_restr | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 25495 |
Nucleic Acid Atoms | |
Solvent Atoms | 23 |
Heterogen Atoms | 462 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
autoPROC | data reduction |
autoPROC | data scaling |
PHASER | phasing |