2HF1
Crystal structure of the putative Tetraacyldisaccharide-1-P 4-kinase from Chromobacterium violaceum. NESG target CvR39.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 291 | 25-35% PEG 300, 0.1M sodium acetate, 5 mM ZnCl(2), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.76 | 30.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 27.517 | α = 90 |
b = 93.854 | β = 90 |
c = 87.219 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 | CCD | ADSC QUANTUM 4 | 2006-06-08 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X4A | 0.97907, 0.97940, 0.96791 | NSLS | X4A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.9 | 31.9 | 99.8 | 0.046 | 6.8 | 17246 | 17211 | 19.6 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.9 | 1.97 | 0.274 | 6.9 | 4.6 | 1750 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | MAD | THROUGHOUT | 1.9 | 26.41 | 2 | 16176 | 16173 | 660 | 93.9 | 0.233 | 0.233 | 0.2465 | 0.284 | 0.3028 | RANDOM | 31.7 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
-2.93 | 0.64 | 2.29 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 25 |
c_angle_deg | 1.4 |
c_improper_angle_d | 0.92 |
c_bond_d | 0.006 |
c_bond_d_na | |
c_bond_d_prot | |
c_angle_d | |
c_angle_d_na | |
c_angle_d_prot | |
c_angle_deg_na |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 925 |
Nucleic Acid Atoms | |
Solvent Atoms | 52 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
SnB | phasing |
RESOLVE | phasing |