Neutron crystal structure of human MTH1(G2K/C87A/C104S mutant) in complex with 2-oxo-dATP
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 5GHJ | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION | 293 | sodium citrate, cacodylate, NaCl | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.89 | 35.02 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 46.386 | α = 90 |
| b = 47.421 | β = 90 |
| c = 123.894 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 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 | PIXEL | DECTRIS PILATUS3 6M | 2019-06-05 | M | SINGLE WAVELENGTH | ||||||
| 2 | 1 | neutron | 100 | DIFFRACTOMETER | iBIX | 2019-03-06 | L | LAUE | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-5A | 1 | Photon Factory | BL-5A |
| 2 | SPALLATION SOURCE | J-PARC MLF BEAMLINE BL-03 | 2.93-5.37 | JPARC MLF | BL-03 |
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 | 1.5 | 37.66 | 99.8 | 0.035 | 36.4 | 6.5 | 44748 | 10.07 | |||||||||||
| 2 | 2.1 | 19.75 | 98.5 | 0.22 | 7.8 | 5.4 | 16382 | 10.07 | |||||||||||
| 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 | 1.5 | 1.59 | 0.075 | ||||||||||||||||
| 2 | 2.1 | 2.21 | 0.533 | ||||||||||||||||
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 | FOURIER SYNTHESIS | 1.5 | 37.65 | 1.4 | 44602 | 2235 | 99.9 | 0.1764 | 0.1749 | 0.1753 | 0.2065 | 0.2073 | 18.89 | ||||||
| NEUTRON DIFFRACTION | FOURIER SYNTHESIS | 2.1 | 19.75 | 16235 | 98.5 | 0.246 | |||||||||||||
| 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] | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 20.909 |
| f_angle_d | 1.0366 |
| f_chiral_restr | 0.0595 |
| f_bond_d | 0.0077 |
| f_plane_restr | 0.0061 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2510 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 288 |
| Heterogen Atoms | 66 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| PHENIX | refinement |
| PHENIX | phasing |
| HKL-2000 | data reduction |
| XDS | data scaling |
