2JE5
STRUCTURAL AND MECHANISTIC BASIS OF PENICILLIN BINDING PROTEIN INHIBITION BY LACTIVICINS
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2BG1 | PDB ENTRY 2BG1 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7 | 50 MH HEPES 3.2 M SODIUM CHLORIDE 0.8 M AMMONIUM SULFATE, pH 7 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.69 | 66.42 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 98.54 | ¦Á = 90 |
b = 99.83 | ¦Â = 90 |
c = 152.16 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | ADSC CCD | 2006-02-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-2 | ESRF | ID14-2 |
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 | 2.6 | 84.52 | 99.2 | 0.1 | 11.46 | 4.7 | 46529 | 5 |
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 | 2.6 | 2.67 | 100 | 0.36 | 4.9 | 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 | PDB ENTRY 2BG1 | 2.6 | 84.52 | 44214 | 2315 | 99.3 | 0.262 | 0.26 | 0.298 | RANDOM | 38.22 |
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] | |
-0.52 | 0.49 | 0.03 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.221 |
r_dihedral_angle_3_deg | 22.119 |
r_dihedral_angle_4_deg | 18.478 |
r_dihedral_angle_1_deg | 8.796 |
r_scangle_it | 6.51 |
r_scbond_it | 4.468 |
r_angle_refined_deg | 3.252 |
r_mcangle_it | 2.749 |
r_mcbond_it | 1.676 |
r_nbtor_refined | 0.341 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7099 |
Nucleic Acid Atoms | |
Solvent Atoms | 79 |
Heterogen Atoms | 52 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
AMoRE | phasing |