7KMU
Structure of WT Malaysian Banana Lectin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2BMY |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293.15 | 1.6M Ammonium Sulfate, 2% Peg 1K, 0.1M HEPES 7.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.34 | 47.53 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.526 | α = 90 |
b = 52.526 | β = 90 |
c = 221.307 | γ = 90 |
Symmetry | |
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Space Group | P 43 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 | CCD | RAYONIX MX300HE | 2017-11-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.9786 | APS | 21-ID-G |
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) | 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 | 1.51 | 50 | 99.5 | 0.06 | 0.062 | 0.016 | 11.5 | 14 | 49873 | 15.54 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.51 | 1.54 | 98.4 | 0.414 | 0.433 | 0.124 | 0.951 | 11.7 |
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 | 2BMY | 1.51 | 42.79 | 49784 | 2464 | 99.5 | 0.183 | 0.182 | 0.202 | RANDOM | 17.25 |
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] | |
0.0645 | 0.0645 | -0.1291 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
t_other_torsion | 14.55 |
t_omega_torsion | 4.27 |
t_angle_deg | 0.99 |
t_bond_d | 0.008 |
t_dihedral_angle_d | |
t_trig_c_planes | |
t_gen_planes | |
t_it | |
t_nbd | |
t_improper_torsion |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2116 |
Nucleic Acid Atoms | |
Solvent Atoms | 363 |
Heterogen Atoms | 16 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data scaling |
BUSTER | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
PHASER | phasing |