2Y2F
Crystal structure of Yersinia pestis YopH in complex with an aminooxy- containing platform compound for inhibitor design
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | MOLECULAR DIMENSIONS MORPHEUS SCREEN CONDITION D8 (0.1M BUFFER SYSTEM 2, PH 7.5, 0.12M ALCOHOLS, 12.5% V/V MPD, 12.5% W/V PEG 1000, 12.5% W/V PEG 3350). |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.04 | 39.57 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.243 | α = 90 |
b = 55.48 | β = 90 |
c = 100.081 | 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 | MARESEARCH MX-300 | 2010-08-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | APS | 22-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 | 1.78 | 50 | 92.8 | 0.11 | 21.9 | 5.9 | 25241 | 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 | 1.78 | 1.8 | 74.8 | 0.5 | 2.3 | 4.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1QZ0 | 1.78 | 50 | 23875 | 1268 | 92.39 | 0.16685 | 0.16457 | 0.21007 | RANDOM | 13.168 |
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] | |
-0.99 | -0.9 | 1.89 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.65 |
r_dihedral_angle_4_deg | 15.855 |
r_dihedral_angle_3_deg | 13.997 |
r_dihedral_angle_1_deg | 5.985 |
r_scangle_it | 4.065 |
r_scbond_it | 2.555 |
r_mcangle_it | 1.54 |
r_angle_refined_deg | 1.487 |
r_angle_other_deg | 0.904 |
r_mcbond_it | 0.813 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2165 |
Nucleic Acid Atoms | |
Solvent Atoms | 274 |
Heterogen Atoms | 22 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |