8AR7
Bovine glutamate dehydrogenase in ternary complex with the allosteric activators ADP and leucine
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 277 | 20% EtOH, 30% 2-methyl-2,4-pentanediol (MPD) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.64 | 53.34 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 90.877 | α = 90 |
b = 178.705 | β = 104 |
c = 123.884 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 PILATUS3 6M | 2021-03-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID30B | 0.97625 | ESRF | ID30B |
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 | 2.448 | 120.203 | 92 | 0.198 | 0.2201 | 0.0945 | 0.989 | 6.82 | 5.37 | 82997 |
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) | ||||||||
2.448 | 2.793 | 60.9 | 1.2113 | 1.3331 | 0.5511 | 0.407 | 1.78 | 5.72 | 4151 |
Refinement
Statistics | |||||||||||||||||||
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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 | 3JCZ | 2.448 | 120.2 | 82997 | 4196 | 59 | 0.193 | 0.1919 | 0.2145 | RANDOM | 68.91 |
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] | |
0.782 | 0.7712 | 1.2819 | -2.064 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 2.69 |
t_omega_torsion | 2.44 |
t_angle_deg | 0.75 |
t_bond_d | 0.006 |
t_dihedral_angle_d | |
t_gen_planes | |
t_it | |
t_chiral_improper_torsion | |
t_ideal_dist_contact |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 22994 |
Nucleic Acid Atoms | |
Solvent Atoms | 439 |
Heterogen Atoms | 222 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
autoPROC | data reduction |
STARANISO | data scaling |
PHASER | phasing |