1R6F
The structure of Yersinia pestis V-antigen, an essential virulence factor and mediator of immunity against plague
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.7 | 294 | PEG 5000 MME, sodium acetate, Tris, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.02 | 39.07 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 35.881 | α = 76.2 |
b = 45.086 | β = 78.42 |
c = 46.915 | γ = 77.17 |
Symmetry | |
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Space Group | P 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 4 | 2002-01-15 | M | MAD | ||||||
2 | 1 | CCD | ADSC QUANTUM 4 | 2002-01-15 |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X9A | 0.9795, 0.9790, 0.9719 | NSLS | X9A |
2 | SYNCHROTRON | NSLS BEAMLINE X9B | 0.9715 | NSLS | X9B |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.17 | 18.5 | 95.9 | 0.077 | 0.077 | 12.5 | 2.2 | 14116 | 14116 | -3 | -3 |
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) | |||||||||||
2.17 | 2.25 | 86.2 | 0.37 | 2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution 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 | MAD | 2.17 | 18.5 | 14116 | 14116 | 1383 | 96.22 | 0.224 | 0.224 | 0.217 | 0.284 | Random | 27.251 |
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] | |
-2.29 | 2.2 | -1.8 | -0.4 | -2.91 | 3.82 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 5.237 |
r_scangle_it | 3.068 |
r_scbond_it | 2.124 |
r_angle_refined_deg | 1.877 |
r_mcangle_it | 1.088 |
r_mcbond_it | 0.629 |
r_nbd_refined | 0.307 |
r_xyhbond_nbd_refined | 0.263 |
r_symmetry_vdw_refined | 0.247 |
r_symmetry_hbond_refined | 0.22 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2139 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
SHARP | phasing |