1YH8
Crystal structure of Aquifex aeolicus LpxC deacetylase complexed with palmitate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1P42 | PDB entry 1P42 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 294 | PEG 3350, NaCl, ZnSO4, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.99 | 58.83 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 101.61 | α = 90 |
b = 101.61 | β = 90 |
c = 124.18 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 61 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | IMAGE PLATE | RIGAKU RAXIS IV | 2004-08-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.7 | 50 | 0.115 | 0.115 | 10.4 | 5.83 | 19665 | 1 | 15.7 |
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) | ||||||||||
2.7 | 2.8 | 98.2 | 0.115 | 0.115 | 4.7 | 5.84 | 2012 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 1P42 | 2.7 | 50 | 19524 | 19524 | 1919 | 97.4 | 0.2011 | 0.2011 | 0.201 | 0.239 | RANDOM | 27.7 |
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] | |
-1.63 | 4.52 | -1.63 | 3.26 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 23.3 |
c_scangle_it | 2.86 |
c_mcangle_it | 1.799 |
c_scbond_it | 1.798 |
c_angle_deg | 1.2 |
c_mcbond_it | 1.078 |
c_improper_angle_d | 0.76 |
c_bond_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 4296 |
Nucleic Acid Atoms | |
Solvent Atoms | 119 |
Heterogen Atoms | 44 |
Software
Software | |
---|---|
Software Name | Purpose |
Crystal | data collection |
d*TREK | data reduction |
AMoRE | phasing |
CNS | refinement |
CrystalClear | data reduction |
d*TREK | data scaling |