6QM3
Crystal structure of a calcium- and sodium-bound mouse Olfactomedin-1 disulfide-linked dimer of the Olfactomedin domain and part of coiled coil
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5AMO |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 277 | 0.08 M Mg Acetate, 30% PEG4000, 0.05 M Na Cacodylate pH 6.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.79 | 55.99 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 160.705 | α = 90 |
b = 46.971 | β = 117.435 |
c = 104.952 | 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 PILATUS3 6M | 2018-12-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.9762 | Diamond | I03 |
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 | 1.89 | 75.994 | 92.2 | 0.06 | 0.072 | 0.039 | 0.998 | 10.3 | 3.3 | 29117 | 34.574240918 |
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 | 1.891 | 2.101 | 77.2 | 0.751 | 0.893 | 0.479 | 0.551 | 1.7 | 3.4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 5AMO | 2 | 71.3 | 1.34348608369 | 27170 | 1459 | 60.2576245501 | 0.180557826647 | 0.178664702636 | 0.215627701203 | 49.0864676127 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.6603569489 |
f_angle_d | 0.852317911462 |
f_chiral_restr | 0.0638063696724 |
f_bond_d | 0.00654472407717 |
f_plane_restr | 0.00414724978879 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4321 |
Nucleic Acid Atoms | |
Solvent Atoms | 99 |
Heterogen Atoms | 133 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
PHENIX | refinement |
Aimless | data scaling |
PHASER | phasing |
Coot | model building |