5T50
LIGAND-FREE LECTIN FROM BAUHINIA FORFICATA
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1HQL |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | PROTEIN CONCENTRATION 5-8 MG/ML IN 0.05 M HEPES BUFFER (pH 7.5) AND 0.15 M NACL, PRECIPITANT: 12% (W/W) PEG8000, 8% (W/V) ETHYLENE GLYCOL, 0.1 M HEPES (pH 7.5), DROPLETS RATIO: 1:1 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.49 | 50.58 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 45.991 | α = 90 |
b = 58.004 | β = 90 |
c = 190.546 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 MX300-HS | 2015-09-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1.0000 | APS | 22-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.43 | 50 | 95.5 | 0.059 | 8.4 | 4.7 | 90961 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.43 | 1.45 | 63.9 | 0.488 | 0.759 | 2.5 |
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 | 1HQL | 1.43 | 30 | 81670 | 4257 | 89.84 | 0.1186 | 0.1164 | 0.1605 | RANDOM | 17.109 |
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] | |
-0.2 | -0.39 | 0.59 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 33.788 |
r_dihedral_angle_2_deg | 33.177 |
r_dihedral_angle_4_deg | 18.571 |
r_dihedral_angle_3_deg | 12.89 |
r_sphericity_bonded | 11.627 |
r_dihedral_angle_1_deg | 7.285 |
r_rigid_bond_restr | 5.757 |
r_mcangle_it | 2.391 |
r_mcbond_it | 2.294 |
r_mcbond_other | 2.225 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3622 |
Nucleic Acid Atoms | |
Solvent Atoms | 395 |
Heterogen Atoms | 36 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data collection |
HKL-3000 | data scaling |
PDB_EXTRACT | data extraction |
HKL-3000 | data reduction |
PHASER | phasing |