4WV8
Crystal structure of a recombinant Vatairea macrocarpa seed lectin complexed with lactose
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | Jeffamine 50% |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.77 | 55.52 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 152.644 | α = 90 |
b = 97.427 | β = 94.68 |
c = 78.667 | 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 | 100 | PIXEL | DECTRIS PILATUS 6M | 2013-10-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | 0.872 | ESRF | ID23-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.83 | 82.045 | 99.4 | 0.081 | 0.097 | 0.054 | 10.6 | 3.1 | 100813 | 100813 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.83 | 1.93 | 98.6 | 0.262 | 0.262 | 0.178 | 2.9 | 3.1 | 14594 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1FNY | 1.83 | 82.045 | 95781 | 5032 | 99.37 | 0.1586 | 0.1567 | 0.1946 | RANDOM | 16.3 |
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] | |
0.56 | 0.39 | -0.52 | -0.1 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.092 |
r_dihedral_angle_4_deg | 17.35 |
r_dihedral_angle_3_deg | 13.501 |
r_dihedral_angle_1_deg | 6.784 |
r_mcangle_it | 2.315 |
r_angle_refined_deg | 1.88 |
r_mcbond_it | 1.542 |
r_mcbond_other | 1.54 |
r_angle_other_deg | 0.891 |
r_chiral_restr | 0.126 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7342 |
Nucleic Acid Atoms | |
Solvent Atoms | 691 |
Heterogen Atoms | 100 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SCALA | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |
XDS | data reduction |