Perdeuterated E65Q-TIM complexed with 2-PHOSPHOGLYCOLIC ACID
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2VXN | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION | 5.4 | 293.15 | 0.1 M sodium acetate, 1 mM Na EDTA, 1 mM DTT,18% PEG6000 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.44 | 49.63 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 98.341 | α = 90 |
| b = 52.365 | β = 118.03 |
| c = 58.463 | 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 | 293 | CCD | ADSC QUANTUM 315 | 2018-04-23 | M | SINGLE WAVELENGTH | ||||||
| 2 | 1 | neutron | 293 | IMAGE PLATE | CUSTOM-MADE | 2018-03-28 | L | LAUE | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE BM30A | 0.98 | ESRF | BM30A |
| 2 | NUCLEAR REACTOR | ILL BEAMLINE LADI III | 2.7-3.5 | ILL | LADI III |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | 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 | 1.15 | 45.674 | 99.4 | 0.049 | 0.999 | 23.49 | 4.9 | 95584 | |||||||||||
| 2 | 1.7 | 40 | 88.6 | 0.097 | 0.997 | 13.3 | 6.6 | 25565 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
| 1 | 1.15 | 1.18 | 0.767 | 2.47 | |||||||||||||||
| 2 | 1.7 | 1.79 | 0.367 | 0.924 | 5.4 | ||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | 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 | 1.15 | 25.3325 | 1.35 | 95574 | 1998 | 99.48 | 0.1405 | 0.1402 | 0.1399 | 0.1528 | 0.1533 | 27.7066 | ||||||
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 1.7 | 30.3961 | 25544 | 533 | 88.01 | 0.1829 | 0.1821 | 0.223 | ||||||||||
| 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] | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1858 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 434 |
| Heterogen Atoms | 11 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| PHENIX | refinement |
| CNS | refinement |
| XDS | data reduction |
| LAUEGEN | data reduction |
| XSCALE | data scaling |
| SCALA | data scaling |
| PHASER | phasing |
