6ZZP
Crystal structure of (R)-3-hydroxybutyrate dehydrogenase from Psychrobacter arcticus complexed with NAD+ and 3-oxovalerate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 298 | 0.18 M succinic acid, 17.2% PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.33 | 47.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68.753 | α = 90 |
b = 111.132 | β = 90 |
c = 137.3 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | 175 | PIXEL | DECTRIS EIGER2 X 16M | 2018-05-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.9763 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.84 | 29.64 | 99.5 | 0.14 | 0.057 | 0.997 | 12 | 6.5 | 90721 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.84 | 1.88 | 89.88 | 0.943 | 0.406 | 0.738 | 2.1 | 2.1 |
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 | D_1292104350 | 1.84 | 29.64 | 86146 | 4528 | 99.41 | 0.1479 | 0.1457 | 0.1893 | RANDOM | 20.873 |
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] | |
2.5 | -1.15 | -1.35 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.381 |
r_dihedral_angle_4_deg | 20.556 |
r_dihedral_angle_3_deg | 13.435 |
r_dihedral_angle_1_deg | 7.72 |
r_angle_other_deg | 1.415 |
r_angle_refined_deg | 1.412 |
r_chiral_restr | 0.07 |
r_gen_planes_refined | 0.012 |
r_bond_refined_d | 0.008 |
r_gen_planes_other | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7500 |
Nucleic Acid Atoms | |
Solvent Atoms | 1022 |
Heterogen Atoms | 216 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |