5UJU
Crystal structure of NAD-dependent aldehyde dehydrogenase from Burkholderia multivorans
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3RJL | PDB entry 3rjl |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 290 | RigakuReagents JCSG+ screen, E1: 100mM Sodium citrate tribasic, 100mM Sodium cocodylate/HCl pH 6.5: BumuA.00020.h.B1.PS37903 at 19.95mg/ml + 2mM NAD: cryo: 20% EG + 2mM NAD: tray 272909e1, puck LCP4-1. Imidazole tentatively modeled, it was present during purification. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.38 | 48.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 114.43 | α = 90 |
b = 114.43 | β = 90 |
c = 154.52 | γ = 120 |
Symmetry | |
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Space Group | P 62 |
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 | CCD | RAYONIX MX-300 | 2016-11-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
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 | 2.05 | 50 | 99.5 | 0.085 | 0.089 | 0.998 | 15.61 | 8.688 | 71387 | -3 | 31.07 |
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) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.05 | 2.1 | 99.9 | 0.522 | 0.553 | 0.943 | 3.37 | 8.647 | 5285 |
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 | FREE R-VALUE | PDB entry 3rjl | 2.05 | 47.183 | 1.34 | 71301 | 1990 | 99.42 | 0.1496 | 0.1482 | 0.1967 | 38.0455 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 11.156 |
f_angle_d | 0.788 |
f_chiral_restr | 0.054 |
f_bond_d | 0.007 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8314 |
Nucleic Acid Atoms | |
Solvent Atoms | 705 |
Heterogen Atoms | 32 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
XDS | data reduction |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
PHASER | phasing |
Coot | model building |
BALBES | phasing |
MOLREP | phasing |