1YE3
HORSE LIVER ALCOHOL DEHYDROGENASE APOENZYME
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 8ADH | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | MICRODIALYSIS | 8.4 | 278 | 50 mM Tris-HCl, 25% methylpentanediol, pH 8.4, MICRODIALYSIS, temperature 278K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.36 | 47.79 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 55.78 | α = 90 |
| b = 74.29 | β = 90 |
| c = 181.25 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 2 2 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 | CCD | ADSC QUANTUM 4 | 2004-07-23 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 17-ID | 1.000 | APS | 17-ID |
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 | 1.59 | 20.2 | 71.9 | 0.075 | 11.5 | 5.66 | 36732 | 1 | 1 | 25.468 | |||||||||
| 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 | 1.59 | 1.65 | 58 | 0.211 | 4.7 | 5.74 | 2918 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | THROUGHOUT | 8ADH | 1.59 | 20.2 | 1 | 35539 | 1143 | 71.92 | 0.2011 | 0.2011 | 0.19946 | 0.25593 | RANDOM | 35.47 | ||||
| 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] | |
| 0.86 | 1.46 | -2.32 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 36.304 |
| r_dihedral_angle_4_deg | 20.041 |
| r_sphericity_free | 17.858 |
| r_dihedral_angle_3_deg | 14.379 |
| r_sphericity_bonded | 8.267 |
| r_dihedral_angle_1_deg | 5.908 |
| r_scangle_it | 4.532 |
| r_scbond_it | 3.249 |
| r_mcangle_it | 2.218 |
| r_rigid_bond_restr | 1.671 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2785 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 200 |
| Heterogen Atoms | 10 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| d*TREK | data reduction |
| d*TREK | data scaling |
