7WWS
Structure of a triple-helix region of human collagen type III from Trautec
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2CUO |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.2M MgAc2, 0.1M Na cacodylate pH6.5, 20% PEG 8000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.79 | 31.25 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 18.582 | α = 90 |
b = 19.32 | β = 96.886 |
c = 74.234 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | 2022-01-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CLSI BEAMLINE 08ID-1 | 0.7749 | CLSI | 08ID-1 |
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 | 1.3 | 36.85 | 99.9 | 0.02 | 58.8 | 6.5 | 13244 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.3 | 1.32 | 0.041 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2cuo | 1.3 | 24.578 | 13236 | 629 | 99.887 | 0.116 | 0.1144 | 0.1582 | 13.945 |
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] | |
-0.08 | -0.299 | -0.012 | 0.16 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 18.853 |
r_dihedral_angle_3_deg | 10.525 |
r_dihedral_angle_4_deg | 10.07 |
r_rigid_bond_restr | 8.076 |
r_dihedral_angle_1_deg | 5.872 |
r_lrange_it | 4.249 |
r_lrange_other | 4.051 |
r_scangle_it | 3.559 |
r_scangle_other | 3.55 |
r_scbond_it | 2.963 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 522 |
Nucleic Acid Atoms | |
Solvent Atoms | 156 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |