7P4Y
GlnK2 from Methanothermococcus thermolithotrophicus in the apo state at a resolution of 2.3 A
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2J9D |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 291.15 | MtGlnK2 apo was crystallized at a concentration of 30 mg/ml in 25 mM Tris/HCl pH 7.6, 10% glycerol, 2mM dithiothreitol and 500 mM NaCl on a 96-Well MRC 2-Drop Crystallization Plates in polystyrene (SWISSCI). Drop of 0.6 ul of protein was mixed with 0.6 ul of the crystallization solution. The reservoir contained 90 ul of the following crystallization solution 35 % w/v Pentaerythritol ethoxylate (15/4 EO/OH) and 100 mM HEPES pH 7.5. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.7 | 54.48 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 103.461 | α = 90 |
b = 103.46 | β = 90 |
c = 178.491 | γ = 90 |
Symmetry | |
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Space Group | P 2 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 | 2020-02-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06DA | 0.99187 | SLS | X06DA |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.3 | 73.16 | 96.2 | 0.133 | 0.144 | 0.055 | 0.998 | 10.2 | 6.7 | 70360 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.3 | 2.4 | 81.3 | 1.151 | 1.259 | 0.508 | 0.671 | 1.5 | 6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | THROUGHOUT | 2J9D | 2.3 | 73.16 | 85.43 | 70326 | 3625 | 82.04 | 0.233 | 0.2215 | 0.2445 | 37.6095 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9066 |
Nucleic Acid Atoms | |
Solvent Atoms | 104 |
Heterogen Atoms | 13 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
autoPROC | data reduction |
autoPROC | data scaling |
MOLREP | phasing |