2X3L
Crystal Structure of the Orn_Lys_Arg decarboxylase family protein SAR0482 from Methicillin-resistant Staphylococcus aureus
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8 | 20% PEG4000, 0.1 M TRIS-CL, PH8.0, 0.32 M MGCL2, 0.8% ETHYLENE GLYCOL. THE CRYSTAL WAS SOAKED WITH 20 MM SAMARIUM ACETATE AND 5MM PLP. THE CRYSTALS WERE CRYOPROTECTED WITH 22% PEG4000, 0.1M TRIS-CL, PH8.0, 0.3 M MGCL2, 2.0% ETHYLENE GLYCOL, 19% PEG400 DILUTED WITH A 50MM PLP SOLUTION 1:10 (FINAL CONCENTRATIONS ABOUT 17% PEG400 AND 5MM PLP) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.1 | 43 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 50.677 | α = 90 |
b = 137.283 | β = 109.64 |
c = 62.258 | γ = 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 | ADSC CCD | MIRRORS | 2007-11-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-3 | ESRF | ID14-3 |
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 | 29.17 | 99.2 | 0.1 | 10.6 | 3.1 | 50798 |
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 | 2 | 2.05 | 98.7 | 0.46 | 2.7 | 2.9 |
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 | SAD | THROUGHOUT | NONE | 2 | 29.17 | 50798 | 2713 | 99.16 | 0.23132 | 0.22886 | 0.27684 | RANDOM | 9.754 |
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] | |
-0.02 | -0.09 | 0.11 | -0.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 41.348 |
r_dihedral_angle_3_deg | 13.938 |
r_dihedral_angle_4_deg | 7.475 |
r_dihedral_angle_1_deg | 5.65 |
r_scangle_it | 1.609 |
r_scbond_it | 1.164 |
r_angle_refined_deg | 1.125 |
r_angle_other_deg | 0.82 |
r_mcangle_it | 0.626 |
r_mcbond_it | 0.349 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6800 |
Nucleic Acid Atoms | |
Solvent Atoms | 127 |
Heterogen Atoms | 41 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
SHELX | phasing |