3TDQ
Crystal structure of a fimbrial biogenesis protein PilY2 (PilY2_PA4555) from Pseudomonas aeruginosa PAO1 at 2.10 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 293 | 15.00% Glycerol, 0.17M NH4OAc, 25.50% PEG-4000, 0.1M Acetate pH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.33 | 47.15 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 51.156 | α = 90 |
b = 53.582 | β = 90 |
c = 76.667 | γ = 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 | MARMOSAIC 325 mm CCD | Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing) | 2011-07-20 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.97901,0.91162,0.97876 | SSRL | BL11-1 |
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 | 2.1 | 25.556 | 97.4 | 0.049 | 10.94 | 12753 | -3 | 33.782 |
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 | 2.1 | 2.17 | 86.7 | 0.33 | 2.4 |
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 | MAD | THROUGHOUT | 2.1 | 25.556 | 12718 | 620 | 0.1882 | 0.1868 | 0.215 | RANDOM | 40.2619 |
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] | |
2.7312 | -2.4473 | -0.2838 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_omega_torsion | 3.65 |
t_other_torsion | 2.54 |
t_angle_deg | 1.06 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_trig_c_planes | |
t_gen_planes | |
t_it | |
t_nbd | |
t_improper_torsion |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1275 |
Nucleic Acid Atoms | |
Solvent Atoms | 104 |
Heterogen Atoms | 20 |
Software
Software | |
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Software Name | Purpose |
MolProbity | model building |
PDB_EXTRACT | data extraction |
SHELX | phasing |
SHARP | phasing |
XSCALE | data scaling |
BUSTER-TNT | refinement |
XDS | data reduction |
SHELXD | phasing |
BUSTER | refinement |