7O9P
Crystal structure of the Awp3b (adhesin-like wall protein 3b) A-domain from Candida glabrata showing a gadolinium cluster
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 291.15 | 0.2 M magnesium chloride, 0.1 M Tris pH 7.0, 3.0 M sodium chloride crystals soaked with 50 mM gadolinium (III) acetate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.95 | 58.34 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 144.397 | α = 90 |
b = 144.397 | β = 90 |
c = 113.95 | γ = 120 |
Symmetry | |
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Space Group | H 3 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2017-06-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 1.71237 | ESRF | ID29 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.99 | 84.2 | 99.8 | 0.104 | 0.107 | 0.025 | 0.998 | 18.8 | 18.2 | 30650 |
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 | 2 | 2.05 | 99.4 | 0.549 | 0.567 | 0.138 | 0.807 | 16.4 |
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 | SAD | THROUGHOUT | 1.99 | 27.42 | 29914 | 1508 | 99.9 | 0.1705 | 0.1685 | 0.2099 | RANDOM | 32.892 |
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] | |
0.47 | 0.23 | 0.47 | -1.52 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 41.072 |
r_dihedral_angle_4_deg | 21.47 |
r_dihedral_angle_3_deg | 14.332 |
r_dihedral_angle_1_deg | 7.688 |
r_angle_refined_deg | 1.689 |
r_angle_other_deg | 1.375 |
r_chiral_restr | 0.074 |
r_bond_refined_d | 0.014 |
r_gen_planes_refined | 0.009 |
r_gen_planes_other | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2309 |
Nucleic Acid Atoms | |
Solvent Atoms | 290 |
Heterogen Atoms | 41 |
Software
Software | |
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Software Name | Purpose |
Aimless | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CRANK2 | phasing |
XDS | data reduction |