4MLL
The 1.4 A structure of the class D beta-lactamase OXA-1 K70D complexed with oxacillin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1M6K | PDB ENTRY 1M6K |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 298 | 10% (w/v) PEG 6000, 0.1 M NaCl, 0.05 M MES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, temperature 298.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.14 | 42.62 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 50.919 | α = 80.9 |
b = 72.609 | β = 69.87 |
c = 73.446 | γ = 71.44 |
Symmetry | |
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Space Group | P 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 | 2012-03-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 1.1 | APS | 21-ID-D |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.37 | 50 | 94.9 | 0.065 | 9.5 | 3.4 | 187539 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.37 | 1.42 | 91.6 | 0.421 | 3.2 | 3.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | THROUGHOUT | PDB ENTRY 1M6K | 1.37 | 33.23 | 187539 | 178142 | 9375 | 94.75 | 0.16476 | 0.16316 | 0.19581 | RANDOM | 21.186 |
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] | |
0.73 | -0.01 | 0.28 | 0.86 | 0.07 | -1.34 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.055 |
r_dihedral_angle_4_deg | 20.249 |
r_dihedral_angle_3_deg | 13.903 |
r_dihedral_angle_1_deg | 6.705 |
r_scbond_it | 3.474 |
r_mcangle_it | 2.821 |
r_mcbond_it | 2.071 |
r_mcbond_other | 2.07 |
r_angle_refined_deg | 1.66 |
r_angle_other_deg | 0.838 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7884 |
Nucleic Acid Atoms | |
Solvent Atoms | 945 |
Heterogen Atoms | 171 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |