2GEM
2.1A crystal structure of Salmonella tyhpimurium YeaZ, a putative Gram-negative RPF, form-A
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | 22% PEG3350 + 0.2M Sodium Malonate, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 7.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.24 | 44.98 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 40.7 | α = 90 |
b = 40.7 | β = 90 |
c = 464.83 | 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 | MARMOSAIC 225 mm CCD | mirrors | 2004-07-23 | M | MAD | |||||
2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 4 | Beryllium compound refractive lenses + diamond monochromator | 2004-08-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM14 | 0.89843, 0.97925 | ESRF | BM14 |
2 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | 0.93400 | ESRF | ID14-1 |
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 | 2.1 | 30 | 0.036 | 28.3 | 3.3 | 23568 | 28024 | -2 | 29.9 |
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) | |||||||||||
2.1 | 2.18 | 44 | 0.327 | 2.3 | 1.9 | 1188 |
Refinement
Statistics | |||||||||||||||||||
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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 | 2.1 | 29.11 | 23568 | 28024 | 2323 | 84.1 | 0.247 | 0.22 | 0.22 | 0.248 | Random | 42.9 |
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] | |
2.3 | 0.37 | 2.3 | -4.59 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 23.5 |
c_angle_deg | 1.2 |
c_improper_angle_d | 0.76 |
c_bond_d | 0.006 |
c_bond_d_na | |
c_bond_d_prot | |
c_angle_d_na | |
c_angle_d_prot | |
c_dihedral_angle_d_na | |
c_dihedral_angle_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3224 |
Nucleic Acid Atoms | |
Solvent Atoms | 403 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
ProDC | data collection |
DENZO | data reduction |
SOLVE | phasing |
CNS | refinement |
SCALEPACK | data scaling |