6VBB
2.60 Angstrom Resolution Crystal Structure of Peptidase S41 from Acinetobacter baumannii
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 292 | Protein: 12.5 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3; Screen: Classics II (F2), 0.2M Trimethylamine N-oxide, 0.1M Tris pH 8.5, 25% (w/v) PEG 2000 MME. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.52 | 51.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 136.311 | α = 90 |
b = 102.525 | β = 116.28 |
c = 68.035 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | CCD | MARMOSAIC 300 mm CCD | C(111) | 2019-10-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (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 | 2.6 | 30 | 100 | 0.1 | 0.1 | 0.114 | 0.054 | 15.5 | 4.4 | 26039 | -3 | 52.8 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
1 | 2.6 | 2.64 | 100 | 0.757 | 0.757 | 0.864 | 0.412 | 0.804 | 2.1 | 4.4 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 2.6 | 29.43 | 24565 | 1301 | 99.89 | 0.1859 | 0.1831 | 0.2374 | RANDOM | 58.936 |
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] | |
1.21 | 0.63 | -6.3 | 3 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 21.972 |
r_dihedral_angle_3_deg | 8.257 |
r_dihedral_angle_4_deg | 8.218 |
r_dihedral_angle_1_deg | 2.078 |
r_angle_refined_deg | 1.336 |
r_angle_other_deg | 0.358 |
r_chiral_restr | 0.058 |
r_gen_planes_refined | 0.053 |
r_gen_planes_other | 0.05 |
r_bond_refined_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5407 |
Nucleic Acid Atoms | |
Solvent Atoms | 117 |
Heterogen Atoms | 24 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
PHENIX | phasing |