2QDT
Structural Basis for the Broad-Spectrum Inhibition of Metallo-{Beta}-Lactamases: L1- IS38 Complex
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1SML | PDB ENTRY 1SML |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 280 | PEG, AS, PH 6.50, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 100K, temperature 280K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.5 | 51 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 105.319 | α = 90 |
b = 105.319 | β = 90 |
c = 97.96 | 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 | 100 | IMAGE PLATE | MARRESEARCH | 2006-01-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | OTHER | 1.54179 |
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 | 1.86 | 50 | 96.5 | 0.084 | 0.084 | 28.1 | 13.7 | 22311 | 21311 | 2 | 2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2 | 2.11 | 94.2 | 0.404 | 0.404 | 5.5 | 11 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | 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 1SML | 2 | 26.54 | 2 | 2 | 22311 | 20217 | 1092 | 95.94 | 0.17106 | 0.16988 | 0.19249 | RANDOM | 30.524 |
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] | |
0.56 | 0.28 | 0.56 | -0.84 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.247 |
r_dihedral_angle_3_deg | 14.425 |
r_dihedral_angle_4_deg | 13.73 |
r_dihedral_angle_1_deg | 6.069 |
r_scangle_it | 2.805 |
r_scbond_it | 1.875 |
r_angle_refined_deg | 1.406 |
r_mcangle_it | 1.17 |
r_mcbond_it | 1.035 |
r_angle_other_deg | 0.929 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2001 |
Nucleic Acid Atoms | |
Solvent Atoms | 232 |
Heterogen Atoms | 29 |
Software
Software | |
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Software Name | Purpose |
CCP4 | model building |
REFMAC | refinement |
MAR345dtb | data collection |
MOSFLM | data reduction |
SCALA | data scaling |
CCP4 | phasing |