2VMB
The three-dimensional structure of the cytoplasmic domains of EpsF from the Type 2 Secretion System of Vibrio cholerae
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7 | 1UL PROTEIN, 1UL RESERVOIR: 12.5% PEG 400, 200MM CAOAC2, 100MM MES PH 7.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2 | 38.08 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.197 | α = 90 |
b = 53.832 | β = 90 |
c = 89.07 | 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 | MARRESEARCH | MIRRORS | 2007-01-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | SSRL | BL9-2 |
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 | 1.95 | 46.07 | 91.7 | 0.05 | 36 | 12.96 | 16364 |
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 | 1.95 | 2.02 | 59.1 | 0.14 | 10.2 | 8.43 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | SAD | THROUGHOUT | NONE | 1.95 | 46.08 | 15530 | 834 | 91.7 | 0.192 | 0.189 | 0.251 | RANDOM | 25.89 |
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] | |
0.22 | 0.87 | -1.09 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.888 |
r_dihedral_angle_4_deg | 18.157 |
r_dihedral_angle_3_deg | 12.82 |
r_dihedral_angle_1_deg | 4.121 |
r_scangle_it | 2.249 |
r_scbond_it | 1.542 |
r_angle_refined_deg | 1.13 |
r_angle_other_deg | 0.975 |
r_mcangle_it | 0.769 |
r_mcbond_it | 0.558 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1851 |
Nucleic Acid Atoms | |
Solvent Atoms | 207 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
ARP/wARP | model building |
CrystalClear | data scaling |
SHELX | phasing |
SHARP | phasing |
DM | phasing |
ARP/wARP | phasing |
REFMAC | refinement |