6MU9
Beta-lactamase penicillinase from Bacillus megaterium
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 289 | 0.1 M Bis-Tris:HCl buffer, 25% PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2 | 38.51 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 35.307 | α = 97.73 |
b = 42.094 | β = 105.52 |
c = 48.542 | γ = 113.34 |
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 | PIXEL | DECTRIS PILATUS3 X 6M | 2018-10-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.9792 | APS | 19-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 0.97 | 45.01 | 76.9 | 0.037 | 0.043 | 0.022 | 12.7 | 3.8 | 108453 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 0.97 | 0.99 | 24.1 | 0.222 | 0.263 | 0.14 | 0.931 | 9.1 | 3.4 |
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 | 2X71 | 0.97 | 45.01 | 103044 | 5408 | 76.85 | 0.1017 | 0.1011 | 0.1112 | RANDOM | 8.118 |
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] | |
0.29 | -0.08 | -0.29 | -0.01 | -0.1 | 0.09 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.036 |
r_sphericity_free | 26.149 |
r_dihedral_angle_4_deg | 15.119 |
r_dihedral_angle_3_deg | 11.21 |
r_sphericity_bonded | 6.737 |
r_dihedral_angle_1_deg | 5.821 |
r_rigid_bond_restr | 1.867 |
r_angle_refined_deg | 1.49 |
r_angle_other_deg | 0.815 |
r_chiral_restr | 0.094 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2056 |
Nucleic Acid Atoms | |
Solvent Atoms | 430 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
HKL-3000 | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-3000 | data reduction |
HKL-3000 | phasing |