3I11
Cobalt-substituted metallo-beta-lactamase from Bacillus cereus
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.8 | 293 | 0.1 M Sodium cacodylate, 0.1 M Sodium tartrate, 18% PEG 3350. Crystals of the apo-protein were soaked in 1 mM CoSO4, pH 5.8, Vapor diffusion, hanging drop, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.26 | 45.66 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 53.087 | α = 90 |
b = 61.363 | β = 93 |
c = 69.57 | 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 | IMAGE PLATE | MAR scanner 345 mm plate | mirrors | 2008-06-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.45 | 40.129 | 90.8 | 0.057 | 0.057 | 7.418 | 3.5 | 35794 |
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) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1.45 | 1.53 | 84.4 | 0.374 | 0.374 | 2 | 2.6 | 4816 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1.45 | 40.13 | 35794 | 1810 | 90.54 | 0.164 | 0.162 | 0.204 | RANDOM | 26.971 |
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] | |
-0.47 | -1.04 | 1.58 | -1.22 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.964 |
r_dihedral_angle_4_deg | 16.287 |
r_dihedral_angle_3_deg | 13.19 |
r_sphericity_free | 10.3 |
r_dihedral_angle_1_deg | 6.802 |
r_scangle_it | 5.368 |
r_sphericity_bonded | 5.14 |
r_scbond_it | 3.706 |
r_mcangle_it | 2.663 |
r_mcbond_it | 1.829 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1656 |
Nucleic Acid Atoms | |
Solvent Atoms | 238 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
AMoRE | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |