4RX2
A triple mutant in the omega-loop of TEM-1 beta-lactamase changes the substrate profile via a large conformational change and an altered general base for catalysis
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1BTL | PDB ENTRY 1BTL |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 298 | 0.1M HEPES pH6.5, 30% W/V PEG 6,000, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.09 | 41.03 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 60.32 | α = 90.06 |
b = 83.3 | β = 89.97 |
c = 95.92 | γ = 90.02 |
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 | 200 | CCD | ADSC QUANTUM 315r | 2013-12-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.1 | 0.997 | ALS | 5.0.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.315 | 62.89 | 75 | 21570 | 21750 | 2 | 2 |
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 | 2.315 | 2.4 | 99.3 | 0.481 | 3.1 |
Refinement
Statistics | |||||||||||||||||||
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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 | THROUGHOUT | PDB ENTRY 1BTL | 2.315 | 62.89 | 76898 | 4081 | 99.63 | 0.23667 | 0.23501 | 0.26795 | RANDOM | 21.496 |
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] | |
0.06 | 0.01 | -0.64 | -0.28 | -0.17 | 0.22 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.024 |
r_dihedral_angle_3_deg | 16.308 |
r_dihedral_angle_4_deg | 16.083 |
r_dihedral_angle_1_deg | 6.133 |
r_long_range_B_refined | 5.447 |
r_long_range_B_other | 5.31 |
r_scangle_other | 2.678 |
r_mcangle_it | 2.555 |
r_mcangle_other | 2.554 |
r_scbond_it | 1.62 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 15679 |
Nucleic Acid Atoms | |
Solvent Atoms | 817 |
Heterogen Atoms | 40 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
MOLREP | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |