3N9S
Class II fructose-1,6-bisphosphate aldolase from helicobacter pylori in complex with N-(4-hydroxybutyl)- glycolohydroxamic acid bis-phosphate, a competitive inhibitor
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3C52 | PDB enry 3c52 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | hanging drop | 8.5 | 298 | 12% PEG 1000, 12% PEG 8000, 0.2 M Calcium Acetate,50 mM Tris/HOAc, pH 8.5, hanging drop, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 44.12 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 50.959 | α = 90 |
b = 83.436 | β = 90 |
c = 139.985 | 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 | CCD | ADSC QUANTUM 315 | 2009-04-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | 1.0809 | NSLS | X29A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.85 | 71.671 | 98.1 | 0.161 | 8.9 | 7.4 | 50710 | 50710 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1.85 | 1.95 | 97 | 0.013 | 1.284 | 0.6 | 7.5 | 7210 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution 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 | PDB enry 3c52 | 1.85 | 32.28 | 0.01 | 47476 | 3553 | 91.63 | 0.169 | 0.165 | 0.214 | 29.52 |
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] | |
-7.281 | 9.644 | -2.363 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 15.836 |
f_angle_d | 0.96 |
f_chiral_restr | 0.057 |
f_bond_d | 0.006 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4652 |
Nucleic Acid Atoms | |
Solvent Atoms | 990 |
Heterogen Atoms | 44 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
XSCALE | data scaling |