3M6B
Crystal Structure of the Ertapenem Pre-isomerized Covalent Adduct with TB B-lactamase
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3DWZ | pdb entry 3DWZ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | hanging drop | 4.1 | 298 | 0.1 M HEPES, 2 M NH4(H2)PO4, pH 4.1, hanging drop, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.25 | 45.41 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.657 | α = 90 |
b = 67.922 | β = 90 |
c = 75.546 | γ = 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 QUANTUM 210 | 2010-01-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X12C | 1.100 | NSLS | X12C |
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 | 1.3 | 50 | 100 | 0.057 | 21.4 | 7.5 | 63485 | 63485 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.3 | 1.33 | 100 | 0.757 | 1.8 | 5.7 | 4388 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 3DWZ | 1.3 | 26.28 | 60263 | 3222 | 99.96 | 0.149 | 0.147 | 0.176 | RANDOM | 13.287 |
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] | |
0.03 | -0.04 | 0.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.298 |
r_dihedral_angle_4_deg | 21.341 |
r_dihedral_angle_3_deg | 11.508 |
r_dihedral_angle_1_deg | 6.091 |
r_scangle_it | 4.451 |
r_scbond_it | 3.009 |
r_mcangle_it | 1.959 |
r_angle_refined_deg | 1.428 |
r_rigid_bond_restr | 1.292 |
r_mcbond_it | 1.198 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1988 |
Nucleic Acid Atoms | |
Solvent Atoms | 297 |
Heterogen Atoms | 61 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CBASS | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |