5LJL
Streptococcus pneumonia TIGR4 flavodoxin: structural and biophysical characterization of a novel drug target
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5LJI |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 292 | 100mM Bis-Tris pH 5.5 and 200 mM calcium chloride, and 10% glycerol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.73 | 29.05 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 29.871 | ¦Á = 90 |
b = 60.707 | ¦Â = 90 |
c = 61.803 | ¦Ã = 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 | 100 | PIXEL | DECTRIS PILATUS3 S 6M | 2013-05-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.92 | Diamond | I04-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | 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 | 1.6 | 20 | 99.2 | 0.102 | 0.998 | 13.9 | 9.9 | 15310 |
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 | 5Lji | 1.6 | 61.8 | 14837 | 433 | 98.92 | 0.17375 | 0.17257 | 0.21532 | RANDOM | 16.596 |
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] | |
2 | -0.49 | -1.51 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.018 |
r_dihedral_angle_4_deg | 31.757 |
r_dihedral_angle_3_deg | 13.607 |
r_dihedral_angle_1_deg | 5.925 |
r_long_range_B_refined | 5.662 |
r_long_range_B_other | 5.624 |
r_scangle_other | 5.047 |
r_scbond_other | 3.329 |
r_scbond_it | 3.321 |
r_mcangle_other | 2.279 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1121 |
Nucleic Acid Atoms | |
Solvent Atoms | 89 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
MOLREP | phasing |