CRYSTAL STRUCTURE OF THE HLYIIR MUTANT PROTEIN WITH RESIDUES 169-186 SUBSTITUTED BY A LINKER CONTAINING TWO THROMBIN SITES
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2FX0 | PDB ENTRY 2FX0 |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 7.5 | TRIS, SODIUM NITRATE, PEG3350, pH 7.5 | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.06 | 59 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 52.315 | α = 90 |
| b = 70.473 | β = 90 |
| c = 139.238 | γ = 90 |
| Symmetry | |
|---|---|
| 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 | 80 | CCD | ADSC CCD | 2008-07-25 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | ESRF | ID14-4 | |
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 | 2.3 | 25 | 100 | 0.08 | 18.2 | 6.5 | 23639 | 2 | 52.9 | ||||||||||
| 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 | 2.3 | 2.38 | 100 | 0.59 | 3.3 | 6.1 | |||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2FX0 | 2.3 | 24.73 | 22337 | 1194 | 99.73 | 0.18951 | 0.18705 | 0.2 | 0.23613 | 0.26 | RANDOM | 37.202 | ||||
| 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] | |
| 1.99 | -1.53 | -0.46 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 39.362 |
| r_dihedral_angle_4_deg | 21.645 |
| r_dihedral_angle_3_deg | 16.327 |
| r_scangle_it | 7.802 |
| r_scbond_it | 5.251 |
| r_dihedral_angle_1_deg | 4.977 |
| r_mcangle_it | 3.137 |
| r_mcbond_it | 1.728 |
| r_angle_refined_deg | 1.248 |
| r_chiral_restr | 0.092 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2997 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 155 |
| Heterogen Atoms | 4 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
