7UHS
SSX Structure of Metallo Beta-Lactamase L1 with Two Water Molecules in the Active Site
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 289 | Batch crystallization done in polypropylene tubes. 200 ul of the L1 (48 mg/ml) in a buffer 0.015 Tris, 0.1 M KCl, 1.5 mM TCEP, 5 mM ZnCl2 pH 7.0 was added to 200 ul of 0.15 M sodium malonate pH 8.0, 20% (w/v) PEG3350. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.77 | 55.55 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 105.951 | α = 90 |
b = 105.951 | β = 90 |
c = 99.886 | γ = 120 |
Symmetry | |
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Space Group | P 64 2 2 |
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 | 295 | PIXEL | DECTRIS PILATUS3 X 6M | 2019-12-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97918 | APS | 19-ID |
Serial Crystallography
Sample delivery method | ||
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Diffraction ID | Description | Sample Delivery Method |
1 | Nylon Mesh | fixed target |
Fixed Target | ||||||
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Diffraction ID | Description | Sample Holding | Support Base | Motion control | Sample Solvent | |
1 | ALEX mesh holder | nylon mesh | xyz stage | SmarAct Motors viaPMAC start/stop raster over area |
Data Reduction | |||
---|---|---|---|
Diffraction ID | Frames Indexed | Crystal Hits | Total Frames |
1 | 4550 | 5191 | 38500 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 2.2 | 46.8 | 100 | 0.95 | 0.25 | 2.51 | 76.5 | 17385 | 34.26 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.2 | 2.24 | 100 | 0.41 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 7L52 | 2.2 | 46.8 | 1.35 | 17255 | 823 | 99.44 | 0.2231 | 0.2214 | 0.2577 | 45.1 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 15.762 |
f_angle_d | 0.4298 |
f_chiral_restr | 0.0383 |
f_plane_restr | 0.0034 |
f_bond_d | 0.0015 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1981 |
Nucleic Acid Atoms | |
Solvent Atoms | 35 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
MOLREP | phasing |
cctbx.prime | data scaling |
DIALS | data reduction |