7CS0
Aminoglycoside 2'-N-acetyltransferase from Mycolicibacterium smegmatis-Complex with Coenzyme A and Paromomycin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 7CRM |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 295 | 0.2M calcium acetate hydrate, 0.1M HEPES (pH 7.5), 10% (w/v) PEG 8000 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.43 | 49.37 |
Crystal Data
Unit Cell | |
---|---|
Length ( ? ) | Angle ( ? ) |
a = 56.374 | ¦Á = 90 |
b = 56.374 | ¦Â = 90 |
c = 122.866 | ¦Ã = 120 |
Symmetry | |
---|---|
Space Group | P 32 |
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 270 | 2019-11-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PAL/PLS BEAMLINE 7A (6B, 6C1) | 0.97935 | PAL/PLS | 7A (6B, 6C1) |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.05 | 50 | 99.9 | 0.101 | 31.56 | 5.6 | 27416 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.05 | 2.09 | 100 | 0.266 | 5.7 |
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 | FREE R-VALUE | 7CRM | 2.05 | 28.2 | 25966 | 1413 | 99.87 | 0.18564 | 0.18306 | 0.23323 | RANDOM | 22.873 |
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] | |
0.01 | 0.01 | -0.02 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.712 |
r_dihedral_angle_4_deg | 15.923 |
r_dihedral_angle_3_deg | 15.385 |
r_dihedral_angle_1_deg | 7.516 |
r_long_range_B_refined | 6.793 |
r_long_range_B_other | 6.741 |
r_scangle_other | 4.482 |
r_mcangle_it | 3.351 |
r_mcangle_other | 3.351 |
r_scbond_it | 2.806 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2912 |
Nucleic Acid Atoms | |
Solvent Atoms | 248 |
Heterogen Atoms | 199 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |