6UNC
The crystal structure of Phosphopantetheinyl Hydrolase (PptH) from Mycobacterium tuberculosis
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 291.15 | 1.3 M ammonium tartrate dibasic; 0.1 M bis-tris propane pH 7.0 with protein: condition 1:1 (protein: condition) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.18 | 43.65 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 74.19 | α = 90 |
b = 92.534 | β = 90 |
c = 183.626 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 120 | PIXEL | DECTRIS PILATUS3 S 6M | 2019-07-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 0.9793 | APS | 23-ID-D |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 2.5 | 44.87 | 99.4 | 0.094 | 0.111 | 0.059 | 0.996 | 12 | 3.4 | 84008 | 50.87 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.5 | 2.589 | 0.963 | 1.137 | 0.601 | 0.57 | 1.8 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | FREE R-VALUE | 2.5 | 44.86 | 1.35 | 83990 | 4324 | 99.4 | 0.1876 | 0.1858 | 0.2215 | 58.15 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 13.8234 |
f_angle_d | 0.5763 |
f_chiral_restr | 0.0452 |
f_plane_restr | 0.0047 |
f_bond_d | 0.0022 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9030 |
Nucleic Acid Atoms | |
Solvent Atoms | 249 |
Heterogen Atoms | 8 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
HKL-2000 | data reduction |
XDS | data scaling |
HKL-2000 | data scaling |
CRANK2 | phasing |
Coot | model building |