2YJV
Crystal structure of E. coli regulator of ribonuclease activity A (RraA) bound to fragment of DEAD-box protein RhlB
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.4 | 298 | CRYSTALS WERE OBTAINED USING THE HANGING DROP METHOD, BY MIXING IN 1 TO 1 RATIO PROTEIN SAMPLE WITH MOTHER LIQUOR 100 MM SODIUM CITRATE PH 5.4, 32% MPD AND 200 MM AMMONIUM ACETATE AT 25 C. PLATES WERE THEN IMMEDIATELY TRANSFERRED TO 16 C. CRYSTALS WERE DIRECTLY FLASH FROZEN IN LIQUID NITROGEN. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.58 | 52 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 259.63 | α = 90 |
b = 69.07 | β = 109.17 |
c = 123.3 | 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 | ADSC CCD | MIRRORS | 2010-03-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I02 | Diamond | I02 |
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 | 2.8 | 63.53 | 98 | 0.05 | 15.5 | 2.9 | 47500 | 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) | |||||||||||
1 | 2.8 | 2.95 | 99.3 | 0.26 | 3.7 | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1Q5X | 2.8 | 122.62 | 47500 | 2535 | 97.52 | 0.22434 | 0.22087 | 0.28774 | RANDOM | 57.396 |
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] | |
0.15 | 1.25 | 2.63 | -1.96 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.472 |
r_dihedral_angle_3_deg | 19.141 |
r_dihedral_angle_4_deg | 18.07 |
r_dihedral_angle_1_deg | 6.619 |
r_scangle_it | 3.003 |
r_scbond_it | 1.647 |
r_angle_refined_deg | 1.507 |
r_mcangle_it | 1.226 |
r_mcbond_it | 0.695 |
r_chiral_restr | 0.1 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 14380 |
Nucleic Acid Atoms | |
Solvent Atoms | 65 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |