4AM9
CRYSTAL STRUCTURE OF THE YERSINIA ENTEROCOLITICA TYPE III SECRETION CHAPERONE SYCD IN COMPLEX WITH A PEPTIDE OF THE TRANSLOCATOR YOPD
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2VGY | PDB ENTRY 2VGY |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 293 | RESERVOIR SOLUTION: 50 MM MES PH 6, 50 MM CITRATE PH 5, 1.1-1.4 M (NH4)2SO4. VAPOR DIFFUSION AT 293 K WITH DROP RATIO OF 1 TO 0.5 PROTEIN TO RESERVOIR. PROTEIN CONCENTRATION 8 MG/ML. 1.3 FOLD MOLAR EXCESS OF PEPTIDE OVER PROTEIN. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.82 | 74.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 106.369 | α = 90 |
b = 106.369 | β = 90 |
c = 51.998 | γ = 120 |
Symmetry | |
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Space Group | P 31 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 | 2011-06-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.2 | BESSY | 14.2 |
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 | 2.5 | 25 | 99.4 | 0.11 | 18.5 | 14 | 11931 | 69.59 |
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 | 2.5 | 2.64 | 97 | 0.57 | 3.1 | 10 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB ENTRY 2VGY | 2.5 | 23.676 | 1.34 | 11901 | 588 | 99.32 | 0.1921 | 0.1899 | 0.2381 | 79.2 |
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] | |
5.2738 | 5.2738 | -10.5477 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 16.576 |
f_angle_d | 1.061 |
f_chiral_restr | 0.069 |
f_bond_d | 0.007 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1116 |
Nucleic Acid Atoms | |
Solvent Atoms | 17 |
Heterogen Atoms | 35 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |