7ZKM
X-ray structure of the complex between human alpha thrombin and a pseudo-cyclic thrombin binding aptamer (TBA-NNp/DDp) - Crystal form beta
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 293 | PEG 4000 20% w/v, 2-propanol 20% v/v, trisodium citrate 0.1 M, pH 5.6 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 48.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 76.6 | α = 90 |
b = 76.6 | β = 90 |
c = 129.38 | γ = 120 |
Symmetry | |
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Space Group | P 31 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 PILATUS 6M | 2020-12-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ELETTRA BEAMLINE 11.2C | 1.0000 | ELETTRA | 11.2C |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 2 | 59.1 | 99.8 | 1 | 23.7 | 18.1 | 30224 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2 | 2.04 | 100 | 0.8 | 2.2 |
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 | 1PPB | 2 | 59.1 | 28692 | 1532 | 99.82 | 0.2275 | 0.2262 | 0.2523 | RANDOM | 62.661 |
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] | |
0.19 | 0.09 | 0.19 | -0.61 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.301 |
r_dihedral_angle_4_deg | 17.964 |
r_dihedral_angle_3_deg | 17.141 |
r_dihedral_angle_1_deg | 7.251 |
r_angle_refined_deg | 1.531 |
r_chiral_restr | 0.117 |
r_bond_refined_d | 0.008 |
r_gen_planes_refined | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2250 |
Nucleic Acid Atoms | 562 |
Solvent Atoms | 44 |
Heterogen Atoms | 259 |
Software
Software | |
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Software Name | Purpose |
autoPROC | data processing |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XSCALE | data scaling |
XDS | data reduction |