8UN9
Crystal structure of the MrfB exonuclease catalytic core
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 289 | The MrfB catalytic core (33-279) was crystallized by hanging drop with 1 microliter of 10 mg/mL protein (in 25 mM Tris pH 7.5, 125 mM NaCl, 1 mM TCEP, 5 mM MgCl2, 2 mM dTMP) and 1 microliter of well solution (0.1 M HEPES pH 7.5, 15% PEG Smear medium, 8% ethylene glycol). Crystals were harvested in 20 mM Tris pH 7.5, 125 mM NaCl, 1 mM TCEP, 5 mM MgCl2, 2 mM dTMP, 0.1 M HEPES pH 7.5, 20% PEG smear medium, and cryoprotected with the addition of 25% ethylene glycol |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.21 | 44.29 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 72.874 | α = 90 |
b = 37.928 | β = 99.147 |
c = 92.616 | 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 | 289 | PIXEL | DECTRIS EIGER X 9M | 2023-02-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 1.127129 | APS | 21-ID-D |
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 | 2.1 | 45.72 | 99.6 | 0.064 | 0.076 | 0.04 | 0.998 | 14.2 | 6.5 | 29515 |
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 | 2.1 | 2.16 | 97.7 | 0.489 | 0.576 | 0.303 | 0.917 | 2.7 | 6.7 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.103 | 41.74 | 29500 | 1471 | 99.588 | 0.178 | 0.1749 | 0.2325 | Random | 51.814 |
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] | |
-0.623 | 0.36 | 2.184 | -1.595 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_6_deg | 15.353 |
r_dihedral_angle_3_deg | 14.997 |
r_lrange_it | 7.96 |
r_lrange_other | 7.919 |
r_dihedral_angle_1_deg | 6.358 |
r_scangle_it | 5.939 |
r_scangle_other | 5.938 |
r_dihedral_angle_2_deg | 5.572 |
r_mcangle_other | 4.119 |
r_mcangle_it | 4.117 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3766 |
Nucleic Acid Atoms | |
Solvent Atoms | 241 |
Heterogen Atoms | 2 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
DIALS | data reduction |
DIALS | data scaling |
PHASER | phasing |