8A9M
Hippeastrum hybrid agglutinin, HHA, complex with beta-mannose
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1MSA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | 50mM PBS, 2M Ammonium sulphate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.29 | 62.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 73.37 | α = 90 |
b = 100.318 | β = 137.27 |
c = 62.177 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | 293 | IMAGE PLATE | MAR scanner 300 mm plate | 1993-04-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SRS BEAMLINE PX9.6 | 0.8975 | SRS | PX9.6 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.2 | 23.82 | 98.5 | 0.133 | 0.148 | 0.063 | 0.986 | 8.2 | 4.9 | 15296 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.2 | 2.27 | 99.5 | 0.389 | 0.436 | 0.191 | 0.896 | 4.7 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | 1MSA | 2.2 | 23.82 | 14531 | 765 | 98.3 | 0.1691 | 0.1665 | 0.2191 | RANDOM | 39.862 |
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] | |
-0.45 | 1.3 | -5.34 | 0.89 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.674 |
r_dihedral_angle_3_deg | 15.386 |
r_dihedral_angle_4_deg | 11.191 |
r_dihedral_angle_1_deg | 8.601 |
r_angle_refined_deg | 1.474 |
r_angle_other_deg | 1.218 |
r_chiral_restr | 0.055 |
r_bond_refined_d | 0.011 |
r_gen_planes_refined | 0.008 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1658 |
Nucleic Acid Atoms | |
Solvent Atoms | 46 |
Heterogen Atoms | 49 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
Aimless | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |