4FBR
Crystal structure of the Myxococcus Xanthus hemagglutinin (MBHA)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3S5V | PDB entry 3S5V |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 298 | 0.2 M ammonium sulphate, 0.1 M sodium cacodylate trihydrate (pH 6.5) and 30% polyethylene glycol 8000, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.25 | 45.43 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 76.099 | α = 90 |
b = 76.099 | β = 90 |
c = 37.667 | γ = 120 |
Symmetry | |
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Space Group | P 31 |
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 | 93 | CCD | RIGAKU SATURN 944 | 2011-06-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E SUPERBRIGHT | 1.5418 |
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 | 1.6 | 32.95 | 97 | 0.094 | 13.2 | 6.48 | 32197 | 31241 | 1 | 2.2 |
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 | 1.6 | 1.66 | 88.8 | 0.406 | 2.2 | 3.65 | 2993 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | 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 | THROUGHOUT | PDB entry 3S5V | 1.6 | 32.95 | 2.2 | 28963 | 28106 | 3126 | 97.04 | 0.18137 | 0.18137 | 0.17794 | 0.21172 | RANDOM | 29.851 |
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] | |
-0.43 | -0.21 | -0.43 | 0.64 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 42.851 |
r_dihedral_angle_4_deg | 12.033 |
r_dihedral_angle_3_deg | 11.994 |
r_dihedral_angle_1_deg | 6.234 |
r_scangle_it | 2.249 |
r_scbond_it | 1.561 |
r_angle_refined_deg | 1.396 |
r_mcangle_it | 1.244 |
r_mcbond_it | 0.76 |
r_chiral_restr | 0.104 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1963 |
Nucleic Acid Atoms | |
Solvent Atoms | 243 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
StructureStudio | data collection |
PHASER | phasing |
REFMAC | refinement |
d*TREK | data reduction |
d*TREK | data scaling |