2IOD
Binding of two substrate analogue molecules to dihydroflavonol-4-reductase alters the functional geometry of the catalytic site
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.9 | 298 | 50mM NaCl, 29% PEG3350, 100mM Hepes, 3mM NaN3, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.49 | 50.69 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 47.231 | α = 90 |
| b = 177.958 | β = 104.77 |
| c = 92.597 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 1 |
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 210 | MIRRORS | 2005-11-19 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 1.0400 | ESRF | ID29 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.06 | 89.535 | 99 | 0.093 | 0.093 | 4 | 3.2 | 89953 | 30 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 2.06 | 2.17 | 94.1 | 0.505 | 0.505 | 2.1 | 2.5 | 12398 | ||||||||||||
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | pdb entry 2c29 | 2.06 | 89.44 | 89894 | 4501 | 98.88 | 0.193 | 0.193 | 0.189 | 0.257 | RANDOM | 35.307 | |||||
| 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] | |
| 0.17 | -0.85 | 2.1 | -2.7 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 30.877 |
| r_dihedral_angle_3_deg | 15.464 |
| r_dihedral_angle_4_deg | 15.034 |
| r_dihedral_angle_1_deg | 5.81 |
| r_angle_other_deg | 4.316 |
| r_mcangle_it | 3.877 |
| r_scangle_it | 3.828 |
| r_scbond_it | 2.778 |
| r_mcbond_it | 2.568 |
| r_angle_refined_deg | 1.925 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 9981 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 768 |
| Heterogen Atoms | 376 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SCALA | data scaling |
| AMoRE | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| ProDC | data collection |
| MOSFLM | data reduction |
