3DD6
Crystal structure of Rph, an exoribonuclease from Bacillus anthracis at 1.7 A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1OYR |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 291 | Ammonium sulphate, K/Na tartrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.3 | 46.49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 86.75 | α = 90 |
b = 86.75 | β = 90 |
c = 179.08 | γ = 120 |
Symmetry | |
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Space Group | H 3 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 4 | mirrors | 2006-04-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-3 | 0.931 | ESRF | ID14-3 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.7 | 43.36 | 98.7 | 0.04 | 25.2 | 7.3 | 28380 | 28380 | 27.43 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1.7 | 1.79 | 95.6 | 0.38 | 4.8 | 5.7 | 3948 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1OYR | 1.702 | 34.65 | 26895 | 26895 | 1413 | 98.42 | 0.21384 | 0.21227 | 0.24414 | RANDOM | 20.643 |
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] | |
-0.27 | -0.14 | -0.27 | 0.41 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.699 |
r_dihedral_angle_3_deg | 14.646 |
r_dihedral_angle_4_deg | 14.523 |
r_dihedral_angle_1_deg | 8.631 |
r_scangle_it | 3.499 |
r_scbond_it | 2.235 |
r_angle_refined_deg | 1.462 |
r_mcangle_it | 1.246 |
r_mcbond_it | 0.76 |
r_chiral_restr | 0.099 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1901 |
Nucleic Acid Atoms | |
Solvent Atoms | 144 |
Heterogen Atoms | 25 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
MOLREP | phasing |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |