3FD0
Crystal structure of putative cystathionine beta-lyase involved in aluminum resistance (NP_470671.1) from LISTERIA INNOCUA at 2.12 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 277 | 0.2000M Ca(OAc)2, 10.0000% PEG-8000, 0.1M Imidazole pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.23 | 61.96 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 131.89 | α = 90 |
b = 131.89 | β = 90 |
c = 116.74 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 1 |
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 | MARMOSAIC 300 mm CCD | Adjustable focusing mirrors in K-B geometry | 2008-10-13 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 0.94645,0.97967 | APS | 23-ID-B |
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 | 2.12 | 29.185 | 99.8 | 0.108 | 10.14 | 8.13 | 66693 | -3 | 32.23 |
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 | 2.12 | 2.2 | 99.8 | 0.875 | 1.69 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | MAD | THROUGHOUT | 2.12 | 29.185 | 66656 | 3382 | 99.87 | 0.154 | 0.152 | 0.188 | RANDOM | 34.7 |
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] | |
-0.61 | -0.31 | -0.61 | 0.92 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.198 |
r_dihedral_angle_3_deg | 12.377 |
r_dihedral_angle_4_deg | 11.679 |
r_scangle_it | 6.816 |
r_scbond_it | 4.725 |
r_dihedral_angle_1_deg | 3.559 |
r_mcangle_it | 2.555 |
r_angle_refined_deg | 1.643 |
r_mcbond_it | 1.545 |
r_angle_other_deg | 1.489 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6279 |
Nucleic Acid Atoms | |
Solvent Atoms | 497 |
Heterogen Atoms | 154 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PHENIX | refinement |
SHELX | phasing |
MolProbity | model building |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
SHELXD | phasing |
autoSHARP | phasing |