4KWU
1.9 Angstrom resolution crystal structure of uncharacterized protein lmo2446 from Listeria monocytogenes EGD-e in complex with alpha-D-glucose, beta-D-glucose, magnesium and calcium
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4KMQ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.3 | 295 | crystallization conditions - 0.2 M magnesium formate, 20% (w/v) PEG3350 (The JCSG+ suite: A5), protein - 7.3 mg/mL in 10 mM Tris-HCl pH8.3 500 mM NaCl 5 mM BME, soak/cryo - crystallization conditions + 50% glucose, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.53 | 51.37 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 166.125 | α = 90 |
b = 102.962 | β = 104.93 |
c = 75.006 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 300 mm CCD | Mirror | 2013-03-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 1.0782 | APS | 21-ID-D |
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 | 1.9 | 30 | 98.5 | 0.076 | 15.8 | 3.6 | 94351 | 94351 | -3 | 22.7 |
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 | 1.9 | 1.93 | 97.5 | 0.568 | 2.6 | 3.6 | 4671 |
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 | THROUGHOUT | 4KMQ | 1.9 | 29.92 | 89621 | 89621 | 4730 | 98.36 | 0.13686 | 0.13508 | 0.17075 | RANDOM | 20.468 |
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] | |
0.43 | 1.82 | 0.2 | 0.32 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.062 |
r_dihedral_angle_4_deg | 15.047 |
r_dihedral_angle_3_deg | 10.189 |
r_dihedral_angle_1_deg | 4.417 |
r_scangle_it | 3.589 |
r_scbond_it | 2.335 |
r_angle_refined_deg | 1.573 |
r_mcangle_it | 1.294 |
r_angle_other_deg | 0.872 |
r_mcbond_it | 0.729 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8335 |
Nucleic Acid Atoms | |
Solvent Atoms | 1232 |
Heterogen Atoms | 129 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |