3LR0
Periplasmic domain of the risS sensor protein from Burkholderia pseudomallei, iodide phased at low pH
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.2 | 289 | Crystal originally grown in JCSG+ condition a6, 0.1M phosphate-citrate pH 4.2, 0.2 M lithium sulfate, 25% PEG 1000 then soaked and cryo-protected into 0.1 M Na citrate pH 4.5, 1.0 M KI, 30% PEG 1000 for 1 hour prior to vitrification; crystal tracking IDs 203087a6 for growth and 206239a1 for soak; affinity tag not removed prior to crystallization, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.26 | 45.64 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 58.36 | α = 90 |
b = 58.36 | β = 90 |
c = 75.69 | γ = 120 |
Symmetry | |
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Space Group | P 32 2 1 |
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 | RIGAKU SATURN 944 | 2009-12-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 |
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 | 1.9 | 19.1 | 99.8 | 0.046 | 25.45 | 11.2 | 12212 | 12191 | -3 | 32.657 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.9 | 1.95 | 99.9 | 0.337 | 4.1 | 8.9 | 925 |
Refinement
Statistics | |||||||||||||||||||
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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 | SAD | THROUGHOUT | 1.9 | 19.1 | 12191 | 585 | 99.84 | 0.213 | 0.211 | 0.254 | RANDOM | 18.791 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.46 | 0.23 | 0.46 | -0.69 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.792 |
r_dihedral_angle_4_deg | 20.377 |
r_dihedral_angle_3_deg | 14.385 |
r_dihedral_angle_1_deg | 5.971 |
r_scangle_it | 4.041 |
r_scbond_it | 2.416 |
r_mcangle_it | 1.568 |
r_angle_refined_deg | 1.388 |
r_mcbond_it | 0.864 |
r_chiral_restr | 0.089 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 806 |
Nucleic Acid Atoms | |
Solvent Atoms | 71 |
Heterogen Atoms | 6 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |