3RS6
Crystal structure Dioclea virgata lectin in complexed with X-mannose
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | lectin was resuspended in 1 mM Tris HCl buffer pH 7.0 containing 5 mM CaCl2 and 5 mM MnCl2 in a final concentration of 10 mg mL 1.native lectin was resuspended in Milli-Q water in a final concentration of 12 mg mL 1 and 3 mM of X-Man (5-bromo-4-chloro-3- Appl Biochem Biotechnol indolyl- -D-mannose), VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.48 | 50.46 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 64.55 | α = 90 |
b = 86.69 | β = 90 |
c = 90.28 | γ = 90 |
Symmetry | |
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Space Group | I 2 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 | MAR CCD 165 mm | 2010-02-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | LNLS BEAMLINE D03B-MX1 | 1.42 | LNLS | D03B-MX1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.8 | 21.33 | 99.7 | 23748 | 2 | 2 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.8 | 99.7 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1.8 | 20.93 | 23748 | 22528 | 1211 | 99.54 | 0.19154 | 0.18947 | 0.2322 | RANDOM | 21.491 |
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] | |
-0.02 | 0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.087 |
r_dihedral_angle_3_deg | 15.366 |
r_dihedral_angle_4_deg | 12.614 |
r_dihedral_angle_1_deg | 7.886 |
r_scangle_it | 5.657 |
r_scbond_it | 4.095 |
r_angle_refined_deg | 2.71 |
r_mcangle_it | 2.588 |
r_mcbond_it | 1.542 |
r_chiral_restr | 0.236 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1761 |
Nucleic Acid Atoms | |
Solvent Atoms | 163 |
Heterogen Atoms | 25 |
Software
Software | |
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Software Name | Purpose |
MAR345dtb | data collection |
MOLREP | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |