6PCB
Crystal structure of beta-ketoadipyl-CoA thiolase mutant (H356A) in complex with COA
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 299 | lithium chloride,PEG 6000,tris (pH- 7.3-8.3) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.16 | 43.18 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 110.487 | α = 90 |
b = 115.958 | β = 90 |
c = 128.866 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 EIGER X 16M | 2017-08-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.95 | Australian Synchrotron | MX2 |
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 | 1.61 | 80 | 99.3 | 0.068 | 0.081 | 0.998 | 11.36 | 3.49 | 413663 | 17.8 |
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 | 1.61 | 1.7 | 97.6 | 0.56 | 0.669 | 0.695 | 1.85 | 3.32 |
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 | native structure | 1.61 | 20 | 211061 | 1016 | 99.36 | 0.16072 | 0.16055 | 0.19612 | RANDOM | 22.863 |
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] | |
-0.01 | -0.02 | 0.03 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.031 |
r_dihedral_angle_4_deg | 15.761 |
r_dihedral_angle_3_deg | 13.37 |
r_dihedral_angle_1_deg | 6.61 |
r_long_range_B_refined | 5.361 |
r_scbond_it | 3.182 |
r_mcangle_it | 2.252 |
r_mcbond_it | 1.617 |
r_angle_refined_deg | 1.606 |
r_chiral_restr | 0.11 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11685 |
Nucleic Acid Atoms | |
Solvent Atoms | 1324 |
Heterogen Atoms | 221 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
Auto-Rickshaw | phasing |