7ECS
Crystal Structure of Aspergillus terreus Glutamate Dehydrogenase (AtGDH) Complexed With Malonate and NADPH
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5XVX |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 295 | 2.4 M Na malonate pH 7.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.05 | 69.61 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 120.15 | ¦Á = 90 |
b = 153.74 | ¦Â = 90 |
c = 259.88 | ¦Ã = 90 |
Symmetry | |
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Space Group | I 2 2 2 |
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 | IMAGE PLATE | RIGAKU RAXIS IV++ | 2016-07-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 1.74 | 39.39 | 99.9 | 0.1 | 0.11 | 0.99 | 16.72 | 7.2 | 244015 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.74 | 1.84 | 99.1 | 0.83 | 0.9 | 0.76 | 2.39 | 6.53 |
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 | 5XVX | 1.74 | 39.38 | 231826 | 12202 | 99.84 | 0.14043 | 0.13924 | 0.16299 | RANDOM | 20.459 |
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] | |
-1.41 | 0.36 | 1.05 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.773 |
r_dihedral_angle_4_deg | 16.352 |
r_dihedral_angle_3_deg | 12.172 |
r_dihedral_angle_1_deg | 5.942 |
r_long_range_B_refined | 5.926 |
r_long_range_B_other | 5.765 |
r_scangle_other | 4.604 |
r_scbond_it | 3.287 |
r_scbond_other | 3.287 |
r_mcangle_it | 2.329 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10401 |
Nucleic Acid Atoms | |
Solvent Atoms | 1742 |
Heterogen Atoms | 330 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |