2P94
Factor xa in complex with the inhibitor 3-chloro-N-((1R,2S)-2-(4-(2-oxopyridin-1(2H)-yl)benzamido)cyclohexyl)-1H-indole-6-carboxamide
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 277 | 200 mM Sodium Acetate, pH 5.5, 18% PEG6000, vapor diffusion, hanging drop, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.53 | 51.45 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 57.029 | α = 90 |
b = 72.546 | β = 90 |
c = 78.489 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | IMAGE PLATE | RIGAKU RAXIS IV++ | BLUE CONFOCAL | 2003-08-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.61 | 34.52 | 83.4 | 0.133 | 5.1 | 3.02 | 36051 | 8.3 |
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) | |||||||||||
1.66 | 1.73 | 49 | 0.37 | 1.8 | 3.35 | 4522 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | MR | THROUGHOUT | 1.8 | 34.52 | 30461 | 29918 | 1759 | 97 | 0.297 | 0.295 | 0.33 | RANDOM | 28.5 |
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] | |
-1.79 | -2.91 | 4.69 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.9 |
c_scangle_it | 2.75 |
c_mcangle_it | 2.33 |
c_scbond_it | 1.92 |
c_angle_deg | 1.8 |
c_mcbond_it | 1.44 |
c_improper_angle_d | 0.73 |
c_bond_d | 0.012 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2238 |
Nucleic Acid Atoms | |
Solvent Atoms | 135 |
Heterogen Atoms | 35 |
Software
Software | |
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Software Name | Purpose |
d*TREK | data processing |
CNS | refinement |
PDB_EXTRACT | data extraction |
d*TREK | data reduction |
d*TREK | data scaling |
EPMR | phasing |
CNX | refinement |