3LUP
Crystal structure of fatty acid binding DegV family protein SAG1342 from Streptococcus agalactiae
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 297 | 0.16 M MgCl2, 80 mM Tris-Cl, 24 % PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.29 | 46.36 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 39.321 | ¦Á = 90 |
b = 84.205 | ¦Â = 90 |
c = 87.541 | ¦Ã = 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 315r | 2009-11-02 | M | MAD | ||||||
2 | 1 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97931 | APS | 19-ID |
2 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97945 | APS | 19-ID |
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 | 2.65 | 50 | 100 | 0.127 | 25.3 | 6.9 | 8910 | 8910 | -3 | 55.1 |
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 | 2.65 | 2.7 | 100 | 0.643 | 4.39 | 6.8 | 411 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 2.65 | 50 | 8870 | 8870 | 422 | 99.81 | 0.20019 | 0.20019 | 0.19727 | 0.26525 | RANDOM | 35.92 |
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] | |
3.08 | -0.64 | -2.43 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.255 |
r_dihedral_angle_3_deg | 18.191 |
r_dihedral_angle_4_deg | 15.081 |
r_dihedral_angle_1_deg | 6.466 |
r_scangle_it | 2.566 |
r_scbond_it | 1.495 |
r_angle_refined_deg | 1.303 |
r_mcangle_it | 0.917 |
r_mcbond_it | 0.459 |
r_chiral_restr | 0.084 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2165 |
Nucleic Acid Atoms | |
Solvent Atoms | 42 |
Heterogen Atoms | 26 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | phasing |
SHELXD | phasing |
SHELXE | model building |
MLPHARE | phasing |
DM | model building |
RESOLVE | model building |
Coot | model building |
ARP/wARP | model building |
CNS | refinement |
SBC-Collect | data collection |
HKL-2000 | data reduction |
HKL-3000 | data scaling |
DM | phasing |
RESOLVE | phasing |