3R38
2.23 Angstrom resolution crystal structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase (murA) from Listeria monocytogenes EGD-e
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2RL2 | PDB ENTRY 2RL2 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 297 | 7.6 mg/mL protein in 10 mM Tris-HCl, 0.25 M sodium chloride, 5 mM BME. Crystallization condition: The Classics II Suite condition A5 (0.1 M HEPES, pH 7.5, 2 M ammonium sulfate). Cryo condition: 1:1 v/v 3.6 M ammonium sulfate : 50 % sucrose, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.81 | 56.22 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 144.579 | α = 90 |
b = 51.923 | β = 110.95 |
c = 78.178 | 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 225 mm CCD | Be-Lenses/Diamond Laue Mono | 2011-02-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | APS | 21-ID-F |
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 | 2.23 | 30 | 99.9 | 0.083 | 14.33 | 3.7 | 26370 | 26370 | -3 | 35.6 |
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) | |||||||||||
2.23 | 2.29 | 100 | 0.36 | 3.69 | 3.7 | 1309 |
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 | PDB ENTRY 2RL2 | 2.23 | 29.11 | 25035 | 25035 | 1328 | 98.71 | 0.19841 | 0.19627 | 0.23864 | RANDOM | 38.984 |
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] | |
-3.86 | -0.73 | 0.08 | 3.26 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 17.709 |
r_dihedral_angle_4_deg | 5.724 |
r_dihedral_angle_3_deg | 5.307 |
r_scangle_it | 4.806 |
r_scbond_it | 2.921 |
r_mcangle_it | 1.597 |
r_angle_refined_deg | 1.328 |
r_dihedral_angle_1_deg | 0.96 |
r_mcbond_it | 0.818 |
r_angle_other_deg | 0.769 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3283 |
Nucleic Acid Atoms | |
Solvent Atoms | 184 |
Heterogen Atoms | 51 |
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 |