4EVU
Crystal structure of C-terminal domain of putative periplasmic protein ydgH from S. enterica
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.6 | 295 | 0.1 M Na Citrate , 0.2 M K/Na tartrate, 1.9 M (NH4)2SO4, 5% Glycerol, 1/210 trypsin, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.29 | 46.37 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 39.079 | α = 90 |
b = 52.521 | β = 109.38 |
c = 39.139 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | ADSC QUANTUM 315r | mirrors | 2011-06-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97935 | 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 | 1.45 | 50 | 99.8 | 0.079 | 25.2 | 3.7 | 26432 | 26374 | -3 | 17.2 |
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 | 1.45 | 1.48 | 100 | 0.576 | 2.2 | 3.6 | 1279 |
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 | SAD | THROUGHOUT | 1.45 | 36.92 | 26330 | 26330 | 1271 | 99.21 | 0.13437 | 0.13437 | 0.13257 | 0.17157 | RANDOM | 15.404 |
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] | |
0.08 | -2.93 | 0.26 | -0.34 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.656 |
r_dihedral_angle_3_deg | 13.936 |
r_dihedral_angle_4_deg | 12.726 |
r_scangle_it | 6.257 |
r_dihedral_angle_1_deg | 6.25 |
r_scbond_it | 4.185 |
r_mcangle_it | 3.259 |
r_mcbond_it | 1.979 |
r_rigid_bond_restr | 1.622 |
r_angle_refined_deg | 1.45 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1071 |
Nucleic Acid Atoms | |
Solvent Atoms | 142 |
Heterogen Atoms | 11 |
Software
Software | |
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Software Name | Purpose |
SBC-Collect | data collection |
SHELX | model building |
MLPHARE | phasing |
DM | model building |
ARP/wARP | model building |
Coot | model building |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
SHELX | phasing |
DM | phasing |