1ZTL
Crystal Structure of the Catalytic Domain of Coagulation Factor XI in Complex with N-[4-Guanidino-1-(thiazole-2-carbonyl)-butyl]-2-{6-oxo-5-[(quinolin-8-ylmethyl)-amino]-2-m-tolyl-6H-pyrimidin-1-yl}-acetamide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1ZHR | PDB entry 1ZHR |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 283 | ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.4 | 48.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 121.965 | α = 90 |
b = 121.965 | β = 90 |
c = 121.965 | γ = 90 |
Symmetry | |
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Space Group | I 2 3 |
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 | 123 | IMAGE PLATE | RIGAKU RAXIS IV++ | Blue Osmic Mirrors | 2004-06-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH3R | 1.5418 |
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 | 2.6 | 28.75 | 99.99 | 0.12 | 14.4 | 3.2 | 9444 | 9444 | 25.2 |
Highest Resolution Shell | |||||||||||||||||||
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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) | |||||||||||
2.6 | 2.69 | 100 | 0.366 | 5.3 | 958 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | PDB entry 1ZHR | 2.6 | 28.75 | 9167 | 956 | 97.1 | 0.208 | 0.237 | RANDOM | 22.7 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 24.5 |
c_scangle_it | 2.81 |
c_mcangle_it | 2.26 |
c_scbond_it | 1.87 |
c_mcbond_it | 1.31 |
c_angle_deg | 1.2 |
c_improper_angle_d | 0.74 |
c_bond_d | 0.007 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1882 |
Nucleic Acid Atoms | |
Solvent Atoms | 89 |
Heterogen Atoms | 44 |
Software
Software | |
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Software Name | Purpose |
CNX | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
CNX | phasing |