5UI9
Crystal Structure of an Oxidoreductase from Agrobacterium radiobacter in Complex with NAD+, 2 -hydroxy-2-hydroxymethyl propanoic acid and Magnesium
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | 3.5 M Sodium formate, 5 mM NAD+, 5 mM magnesium chloride |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.38 | 63.59 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 137.881 | α = 90 |
| b = 112.771 | β = 94.7 |
| c = 65.371 | 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 | 100 | CCD | ADSC QUANTUM 315 | Diamond | 2016-10-28 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 31-ID | 0.97931 | APS | 31-ID |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 1.92 | 37.13 | 97.7 | 0.09 | 0.124 | 0.085 | 0.993 | 7.2 | 3.8 | 73981 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 1.92 | 2.02 | 97.1 | 1.194 | 1.613 | 1.077 | 0.31 | 1.5 | 3.8 | ||||||||||
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 | 5UHW | 1.92 | 37.13 | 70058 | 3703 | 97.19 | 0.18378 | 0.18281 | 0.20221 | RANDOM | 41.266 | ||||||
| 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] | |
| -1.28 | 0.03 | 1.19 | 0.08 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.432 |
| r_dihedral_angle_3_deg | 13.052 |
| r_dihedral_angle_4_deg | 11.578 |
| r_dihedral_angle_1_deg | 5.604 |
| r_long_range_B_refined | 4.23 |
| r_long_range_B_other | 4.193 |
| r_scangle_other | 2.703 |
| r_mcangle_it | 2.041 |
| r_mcangle_other | 2.04 |
| r_scbond_it | 1.69 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 5163 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 227 |
| Heterogen Atoms | 106 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MOSFLM | data reduction |
| Aimless | data scaling |
