3C5A
Crystal structure of the C-terminal deleted mutant of the class A carbapenemase KPC-2 at 1.23 angstrom
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2ODS | PDB ENTRY 2ODS |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4 | 291 | 20% PEG4K, 0.1M KSCN, 0.1M Citrate, VAPOR DIFFUSION, SITTING DROP, pH4.0, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.04 | 39.58 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 47.89 | α = 90 |
b = 65.99 | β = 90 |
c = 72.13 | 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 | 77 | CCD | ADSC QUANTUM 315 | mirror 1, double crystal, mirror 2 | 2007-03-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM30A | 0.979 | ESRF | BM30A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.23 | 27.17 | 97.7 | 22.55 | 13.6 | 65197 | 14.7 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1.23 | 1.31 | 91.9 | 0.196 | 6.5 | 11.6 | 9747 |
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 2ODS | 1.23 | 27.17 | 65188 | 3259 | 100 | 0.182 | 0.181 | 0.196 | RANDOM | 11.796 |
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] | |
0.1 | -0.01 | -0.08 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.311 |
r_dihedral_angle_3_deg | 11.727 |
r_dihedral_angle_4_deg | 9.134 |
r_dihedral_angle_1_deg | 5.739 |
r_scangle_it | 2.07 |
r_scbond_it | 1.398 |
r_angle_refined_deg | 1.139 |
r_mcangle_it | 0.933 |
r_mcbond_it | 0.558 |
r_nbtor_refined | 0.304 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1972 |
Nucleic Acid Atoms | |
Solvent Atoms | 183 |
Heterogen Atoms | 13 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Xnemo | data collection |
XDS | data reduction |
PHASER | phasing |