4P9Y
Structure of ConA/Rh4man
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | LIQUID DIFFUSION | 7.2 | 298 | buffer: 20 mM HEPES, 5 mM of CaCl2, and 5 mM of MnCl2; pH = 7.2. The crystal was obtained by diffusion method in glass tube sequentially put with ConA solution, pure buffer, and the ligand solution. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.05 | 39.94 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 61.6 | α = 90 |
b = 116.11 | β = 90 |
c = 58.69 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | PIXEL | DECTRIS PILATUS 6M | 2013-07-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.918 | BESSY | 14.1 |
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 | 1.89 | 39.9 | 99.9 | 46.74 | 6.68 | 34408 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.89 | 30 | 33322 | 1086 | 99.86 | 0.2025 | 0.2007 | 0.2581 | RANDOM | 16.861 |
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] | |
-1.81 | 3.83 | -2.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.616 |
r_dihedral_angle_4_deg | 18.912 |
r_dihedral_angle_3_deg | 17.022 |
r_dihedral_angle_1_deg | 8.015 |
r_angle_refined_deg | 1.955 |
r_chiral_restr | 0.139 |
r_bond_refined_d | 0.018 |
r_gen_planes_refined | 0.011 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3618 |
Nucleic Acid Atoms | |
Solvent Atoms | 88 |
Heterogen Atoms | 128 |
Software
Software | |
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Software Name | Purpose |
MOLREP | phasing |
PDB_EXTRACT | data extraction |
REFMAC | refinement |
Coot | model building |
XDS | data scaling |