5PAK
Crystal Structure of Factor VIIa in complex with N-[[4-(aminomethyl)-2-(2-amino-2-oxoethoxy)phenyl]methyl]-2-(4-hydroxyphenyl)-2-methoxyacetamide;hydrochloride
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 277 | 16 mg/ml protein in 20mM Tris/HCl pH 8.4, 5 mM benzamidine, 0.1 M NaCl, 50 mM CaCl2 mixed 1+1 with 32-35% AMMONIUM SULPHATE, 2% PEG 4000, 0.1 M Bicine-NaOH pH 8.5, 15% glycerol |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.77 | 67.4 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 95.402 | α = 90 |
| b = 95.402 | β = 90 |
| c = 116.322 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 41 21 2 |
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 | MAR scanner 345 mm plate | 2007-03-19 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | BRUKER AXS MICROSTAR | 1.54178 | ||
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 | 1.56 | 50 | 96.4 | 0.062 | 14.3 | 2.9 | 74176 | ||||||||||||
| 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 | 1.56 | 1.62 | 93.2 | 0.445 | 2.7 | 7059 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | inhouse model | 1.56 | 33.73 | 65645 | 3506 | 89.91 | 0.1861 | 0.1852 | 0.2025 | RANDOM | 17.436 | ||||||
| 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] | |
| -0.26 | -0.26 | 0.53 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 28.98 |
| r_dihedral_angle_4_deg | 19.777 |
| r_dihedral_angle_3_deg | 14.134 |
| r_dihedral_angle_1_deg | 5.797 |
| r_scangle_it | 2.342 |
| r_scbond_it | 1.528 |
| r_angle_refined_deg | 1.181 |
| r_mcangle_it | 1.163 |
| r_angle_other_deg | 0.832 |
| r_mcbond_it | 0.754 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2371 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 389 |
| Heterogen Atoms | 38 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| PHASER | phasing |
