7QTZ
Crystal structure of Iripin-1 serpin from tick Ixodes ricinus
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3NDA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 277 | Nickel(II) sufate hexahydrate, Hepes, Jeffamine M-600 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.49 | 50.66 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 48.819 | α = 90 |
b = 91.005 | β = 97.53 |
c = 95.833 | 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 PILATUS 2M | 2020-04-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.2 | 0.918400 | BESSY | 14.2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.097 | 95.006 | 99.2 | 0.133 | 0.144 | 0.055 | 10.7 | 6.8 | 48379 | 48379 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.1 | 2.21 | 97.7 | 1.09 | 1.09 | 1.179 | 0.446 | 0.7 | 6.8 |
Refinement
Statistics | |||||||||||||||||||
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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 | 3nda | 2.1 | 48.44 | 45891 | 2464 | 99.13 | 0.1933 | 0.1902 | 0.2506 | RANDOM | 38.591 |
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] | |
-0.79 | 0.74 | 2.07 | -1.43 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.081 |
r_dihedral_angle_4_deg | 15.128 |
r_dihedral_angle_3_deg | 14.232 |
r_dihedral_angle_1_deg | 7.669 |
r_angle_refined_deg | 1.417 |
r_angle_other_deg | 1.301 |
r_chiral_restr | 0.064 |
r_bond_refined_d | 0.007 |
r_gen_planes_refined | 0.006 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5629 |
Nucleic Acid Atoms | |
Solvent Atoms | 521 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
MOLREP | phasing |
PDB_EXTRACT | data extraction |