4DLM
Crystal structure of an amidohydrolase (COG3618) from burkholderia multivorans (TARGET EFI-500235) with bound ZN, space group P212121
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | sitting drop vapor diffuction | 8 | 298 | Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol, 0.5 mM ZnCl, 0.5 mM D-arabonate-1,4-lactone; Reservoir (20% Peg3350, 100 mM Tris pH 8.0); Cryoprotection (Reservoir, 5 mM Zn, 25 mM D-arabonate-1,4-lactone, 20% ethylene glycol), sitting drop vapor diffuction, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.16 | 43.01 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 60.86 | α = 90 |
b = 63.2 | β = 90 |
c = 76.22 | 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 | 100 | CCD | ADSC QUANTUM 315r | MIRRORS | 2011-10-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | 0.9793 | 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 | 1.925 | 76.22 | 91.6 | 0.123 | 7.4 | 4.1 | 20778 | 20778 |
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 | 1.92 | 2.03 | 93.7 | 0.651 | 0.651 | 1.2 | 3.9 | 3074 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution 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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.925 | 48.651 | 1.34 | 20750 | 20750 | 1087 | 90.52 | 0.1803 | 0.1773 | 0.2345 | random | 23.9945 |
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] | |
-4.0828 | -0.0028 | 4.0856 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.853 |
f_angle_d | 1.07 |
f_chiral_restr | 0.073 |
f_bond_d | 0.01 |
f_plane_restr | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2268 |
Nucleic Acid Atoms | |
Solvent Atoms | 213 |
Heterogen Atoms | 7 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
CBASS | data collection |
PHENIX | phasing |