8QJN
SmNuc1 nuclease from Stenotrophomonas maltophilia in complex with adenosine-5'-monophosphate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 8QJL | D_1292131829 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 291 | 0.2 M Ammonium sulfate 0.1 M MES pH 6.5, 30% w/v Polyethylene glycol 8000. Protein concentration 8.5 mg/ml. Cryo-protection by glycerol 20 % v/v. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.33 | 47.28 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 44.47 | α = 90 |
b = 72.741 | β = 102.684 |
c = 82.752 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | 2021-10-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.9184 | BESSY | 14.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 1.65 | 43.385 | 88.8 | 0.105 | 0.113 | 0.998 | 13.2 | 6.9 | 52701 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.65 | 1.69 | 92.8 | 0.869 | 0.935 | 0.777 | 2.2 |
Refinement
Statistics | |||||||||||||||||||
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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-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.65 | 43.385 | 52701 | 2536 | 85.069 | 0.176 | 0.1759 | 0.1747 | 0.2143 | Random | 19.032 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.156 | 0.37 | -0.33 | 0.007 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.664 |
r_dihedral_angle_4_deg | 21.353 |
r_dihedral_angle_3_deg | 14.055 |
r_dihedral_angle_1_deg | 6.339 |
r_lrange_it | 6.143 |
r_lrange_other | 5.816 |
r_scangle_it | 3.895 |
r_scangle_other | 3.862 |
r_mcangle_it | 2.561 |
r_mcangle_other | 2.555 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3809 |
Nucleic Acid Atoms | |
Solvent Atoms | 589 |
Heterogen Atoms | 55 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
STARANISO | data scaling |
MOLREP | phasing |
Coot | model building |