4EQI
Crystal structure of serratia fonticola carbapenemase SFC-1
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2OV5 | PDB ENTRY 2OV5 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | Na acetate, PEG 3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.01 | 38.75 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 42.33 | ¦Á = 90 |
b = 85.43 | ¦Â = 103.27 |
c = 70.28 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 1 21 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 | CCD | MARMOSAIC 225 mm CCD | 2008-05-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SRS BEAMLINE PX10.1 | 1.117 | SRS | PX10.1 |
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 | 1.38 | 50 | 99.6 | 0.064 | 18.234 | 3.6 | 99798 | 99419 | 11.3 |
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 | 1.38 | 1.43 | 99.4 | 0.568 | 2.03 | 3.3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | FREE R | PDB ENTRY 2OV5 | 1.38 | 17.85 | 99390 | 93687 | 4966 | 99.5 | 0.141 | 0.14 | 0.188 | RANDOM |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
65 | 3948 | 4913.4 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_non_zero_chiral_vol | 0.062 |
s_zero_chiral_vol | 0.058 |
s_approx_iso_adps | 0.046 |
s_angle_d | 0.029 |
s_from_restr_planes | 0.029 |
s_anti_bump_dis_restr | 0.019 |
s_similar_adp_cmpnt | 0.019 |
s_bond_d | 0.01 |
s_rigid_bond_adp_cmpnt | 0.003 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4180 |
Nucleic Acid Atoms | |
Solvent Atoms | 710 |
Heterogen Atoms | 38 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
PHASER | phasing |
SHELXL-97 | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |