2ZI2
Thrombin Inhibition
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1H8D | PDB entry 1H8D |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 277 | Phosphate Buffer, Sodium Chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.55 | 51.79 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 70.5 | α = 90 |
| b = 71.6 | β = 100.6 |
| c = 72.6 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 1 2 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 110 | CCD | MARMOSAIC 225 mm CCD | 2007-06-29 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.91841 | BESSY | 14.1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.65 | 20 | 96.5 | 0.032 | 20.81 | 2 | 41212 | 41212 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 1.65 | 1.68 | 77.8 | 0.238 | 2.53 | 1.7 | 1681 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R | PDB entry 1H8D | 1.65 | 10 | 39496 | 39496 | 1973 | 92.9 | 0.1876 | 0.1876 | 0.1815 | 0.2246 | RANDOM | |||||
| 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] | |
| Coordinate Error | ||
|---|---|---|
| Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
| 5 | 2545.5 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| s_similar_adp_cmpnt | 0.076 |
| s_non_zero_chiral_vol | 0.059 |
| s_zero_chiral_vol | 0.05 |
| s_from_restr_planes | 0.0271 |
| s_angle_d | 0.026 |
| s_anti_bump_dis_restr | 0.013 |
| s_bond_d | 0.009 |
| s_similar_dist | |
| s_rigid_bond_adp_cmpnt | |
| s_approx_iso_adps | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2320 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 192 |
| Heterogen Atoms | 34 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SHELX | model building |
| SHELXL-97 | refinement |
| MAR345 | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| CNS | phasing |
