2C0B
Catalytic domain of E. coli RNase E in complex with 13-mer RNA
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2BX2 | PDB ENTRY 2BX2 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | 293 | CRYSTALS OF THE RNASE E CATALYTIC DOMAIN/ RNA COMPLEX APPEARED AFTER TWO TO FOUR WEEKS IN 5 TO 20 % WT/V POLYETHYLENE GLYCOL 8,000, 0.1 M TRIS PH 7.5 TO 8.0, AND 10 TO 50 MM MAGNESIUM FORMATE AT 20 C |
Crystal Properties | |
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Matthews coefficient | Solvent content |
6.6 | 82 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 196.049 | α = 90 |
b = 196.049 | β = 90 |
c = 142.66 | γ = 120 |
Symmetry | |
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Space Group | P 62 2 2 |
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 | MARRESEARCH | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | ESRF | ID23-1 |
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 | 3.2 | 25 | 100 | 0.11 | 30 | 15.5 | 27564 |
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 | 3.2 | 3.31 | 96.7 | 0.51 | 5.2 | 15 |
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 2BX2 | 3.18 | 12 | 25508 | 1349 | 99.3 | 0.254 | 0.252 | 0.282 | RANDOM | 43.58 |
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] | |
0.04 | 0.02 | 0.04 | -0.06 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.61 |
r_dihedral_angle_4_deg | 22.263 |
r_dihedral_angle_3_deg | 20.497 |
r_scangle_it | 15.488 |
r_scbond_it | 11.633 |
r_dihedral_angle_1_deg | 7.637 |
r_mcangle_it | 7.194 |
r_mcbond_it | 4.554 |
r_angle_refined_deg | 1.583 |
r_nbd_refined | 0.36 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3555 |
Nucleic Acid Atoms | 214 |
Solvent Atoms | 49 |
Heterogen Atoms | 3 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |