5Y45
Crystal structure of a collagen-like peptide with interruption sequence
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 7 | 293 | 0.1 M HEPES pH 7.0, 30% v/v Jeffamine, M-600 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
1.65 | 25.33 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 13.75 | α = 90 |
b = 45.44 | β = 90.67 |
c = 77.63 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 PILATUS3 S 6M | 2017-04-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL19U1 | 0.9778 | SSRF | BL19U1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.03 | 45.44 | 94.39 | 6.8 | 5.8 | 42193 |
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 | AB INITIO PHASING | THROUGHOUT | 1.03 | 45.44 | 42193 | 2185 | 94.39 | 0.1457 | 0.1441 | 0.1754 | RANDOM | 9.322 |
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] | |
0.36 | -0.38 | -0.11 | -0.24 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 15.079 |
r_dihedral_angle_3_deg | 12.433 |
r_dihedral_angle_1_deg | 6.85 |
r_sphericity_bonded | 6.707 |
r_angle_refined_deg | 2.553 |
r_rigid_bond_restr | 1.741 |
r_angle_other_deg | 1.515 |
r_chiral_restr | 0.09 |
r_bond_refined_d | 0.016 |
r_gen_planes_refined | 0.013 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1044 |
Nucleic Acid Atoms | |
Solvent Atoms | 238 |
Heterogen Atoms | 9 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data collection |
Aimless | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MOSFLM | data collection |
ACORN | phasing |