4FBV
Crystal structure of the Myxococcus Xanthus hemagglutinin in complex with a3,a6-mannopentaose
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4FBR | PDB entry 4FBR |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 298 | 0.05 M monobasic potassium phosphate and 20% w/v polyethylene glycol 3350, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.48 | 50.37 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 45.592 | α = 90 |
b = 57.319 | β = 90 |
c = 105.969 | 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 | 93 | CCD | RIGAKU SATURN 944 | 2011-07-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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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 | 1.76 | 33.82 | 96.8 | 0.053 | 22.1 | 6.63 | 28299 | 27394 | 1 | 3.8 |
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 | 1.76 | 1.82 | 81.5 | 0.206 | 3.8 | 2.53 | 2789 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 4FBR | 1.76 | 33.82 | 3.8 | 26858 | 25993 | 1375 | 96.78 | 0.18764 | 0.18764 | 0.18622 | 0.21368 | RANDOM | 24.264 |
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] | |
-0.37 | 0.91 | -0.54 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.364 |
r_dihedral_angle_3_deg | 10.787 |
r_dihedral_angle_1_deg | 6.392 |
r_dihedral_angle_4_deg | 5.071 |
r_scangle_it | 2.249 |
r_scbond_it | 1.583 |
r_angle_refined_deg | 1.4 |
r_mcangle_it | 1.124 |
r_mcbond_it | 0.684 |
r_chiral_restr | 0.094 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1963 |
Nucleic Acid Atoms | |
Solvent Atoms | 197 |
Heterogen Atoms | 128 |
Software
Software | |
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Software Name | Purpose |
StructureStudio | data collection |
PHASER | phasing |
REFMAC | refinement |
d*TREK | data reduction |
d*TREK | data scaling |