4XGN
Crystal structure of 3-hydroxyacyl-CoA dehydrogenase in complex with NAD from Burkholderia thailandensis
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 290 | Morpheus screen c6: 10% PEG 8000, 20% EG; 30mM each NaNO3, Na2HPO4, (NH4)2SO4; 100mM MOPS/HEPES pH 7.5; ButhA.0010.l.B1.PS01726 at 10mg/ml with 2.5mM NAD; direct cryo; tray 252631c6, puck sxz2-6 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.52 | 51 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 71.22 | α = 103.26 |
b = 77.1 | β = 93.98 |
c = 109.35 | γ = 109.68 |
Symmetry | |
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Space Group | P 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 | CCD | RAYONIX MX-225 | 2014-02-12 | 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) | 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 | 1.65 | 50 | 97.1 | 0.081 | 0.094 | 11.23 | 4 | 253404 | 246070 | -3 | 22.006 |
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) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.65 | 1.69 | 95.4 | 0.476 | 0.55 | 2.88 | 4 |
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 | 3TPC | 1.65 | 50 | 233814 | 12256 | 97.15 | 0.1557 | 0.1545 | 0.1771 | RANDOM | 16.931 |
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] | |
0.29 | -0.56 | 0.22 | -0.19 | -0.01 | 0.23 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.291 |
r_dihedral_angle_4_deg | 17.08 |
r_dihedral_angle_3_deg | 11.797 |
r_dihedral_angle_1_deg | 5.993 |
r_angle_refined_deg | 1.74 |
r_mcangle_it | 1.107 |
r_angle_other_deg | 0.98 |
r_mcbond_it | 0.634 |
r_mcbond_other | 0.633 |
r_chiral_restr | 0.095 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 14506 |
Nucleic Acid Atoms | |
Solvent Atoms | 1923 |
Heterogen Atoms | 468 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |
ARP | model building |
Coot | model building |
REFMAC | refinement |
PDB_EXTRACT | data extraction |