6CAF
High Resolution Structure of Concanavalin B from Jack Bean (Canavalia ensiformis), A Chitinase-like Protein
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 298 | 2% saturated ammonium sulfate buffered with Na phosphate at pH 6.5. Room temperature, crystallization in about 1 week. Protein dissolved in 5% NaCl and 0.1 M acetic acid. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.54 | 51.67 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 79.987 | α = 90 |
b = 79.987 | β = 90 |
c = 101.312 | γ = 120 |
Symmetry | |
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Space Group | P 61 |
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 | 173 | PIXEL | DECTRIS PILATUS3 R CdTe 300K-W | 2016-08-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | 0.987 | ALS | 8.3.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 1.3 | 101.31 | 82 | 0.167 | 0.158 | 0.168 | 0.022 | 1 | 50.1 | 51.5 | 73116 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
1 | 1.3 | 1.33 | 18.1 | 0.85 | 0.78 | 0.918 | 0.331 | 0.71 | 3.6 | 5.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1.3 | 69.27 | 69491 | 3565 | 81.87 | 0.09728 | 0.09574 | 0.12778 | RANDOM | 22.91 |
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] | |
0.03 | 0.02 | 0.03 | -0.11 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 51.038 |
r_dihedral_angle_2_deg | 36.089 |
r_sphericity_bonded | 24.045 |
r_dihedral_angle_4_deg | 23.049 |
r_dihedral_angle_3_deg | 13.081 |
r_scangle_other | 12.951 |
r_long_range_B_refined | 11.774 |
r_long_range_B_other | 11.031 |
r_scbond_other | 10.715 |
r_scbond_it | 10.713 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2298 |
Nucleic Acid Atoms | |
Solvent Atoms | 344 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |