1G9U
CRYSTAL STRUCTURE OF YOPM-LEUCINE RICH EFFECTOR PROTEIN FROM YERSINIA PESTIS
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 10% isopropanol 0.1 M MES, 0.2-0.4 M Ca(OAc)2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 321.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.94 | 58.14 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 109.359 | α = 90 |
b = 109.359 | β = 90 |
c = 101.499 | γ = 90 |
Symmetry | |
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Space Group | P 42 2 2 |
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 4 | synchrotron Si monochromator + Osmic mirrors | 2000-03-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X9B | 0.9879 | NSLS | X9B |
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 | 2.32 | 74 | 81 | 0.1 | 9 | 1.9 | 49157 | 39896 | 4 | 4 | 18 |
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 | 2.32 | 2.45 | 96.4 | 0.43 | 2.2 | 1.8 | 7609 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MIR | random 5% throughout the refinement | new structure | 2.35 | 100 | 43317 | 33478 | 2285 | 97 | 0.21 | 0.17 | 0.2 | 0.23 | random 5% | 33 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_from_restr_planes | 0.34 |
s_angle_d | 0.04 |
s_anti_bump_dis_restr | 0.014 |
s_bond_d | 0.009 |
s_approx_iso_adps |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2793 |
Nucleic Acid Atoms | |
Solvent Atoms | 236 |
Heterogen Atoms | 46 |
Software
Software | |
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Software Name | Purpose |
SOLVE | phasing |
SHELXL-97 | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |