1S03
The Structure of a Ribosomal Protein S8/spc Operon mRNA Complex
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1J5E | PDB entry 1J5E |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.2 | 296 | PEG 8000, zinc acetate, sodium acetate buffer, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.26 | 61.93 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 61.22 | α = 90 |
b = 61.22 | β = 90 |
c = 332.52 | γ = 120 |
Symmetry | |
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Space Group | P 32 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 | M | SINGLE WAVELENGTH | ||||||||||
2 | 1 | |||||||||||||
3 | 1 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X25 | 1.0049 | NSLS | X25 |
2 | SYNCHROTRON | NSLS BEAMLINE X25 | 0.9928 | NSLS | X25 |
3 | SYNCHROTRON | NSLS BEAMLINE X25 | 1.008998 | NSLS | X25 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.7 | 50 | 20950 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.7 | 2.8 | 3907 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 1J5E | 2.7 | 50 | 2 | 19880 | 1070 | 99.8 | 0.23917 | 0.23734 | 0.23734 | 0.27313 | RANDOM | 44.626 |
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] | |
0.01 | 0.01 | 0.01 | -0.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 6.905 |
r_scangle_it | 5.825 |
r_scbond_it | 3.798 |
r_mcangle_it | 3.773 |
r_angle_refined_deg | 2.331 |
r_mcbond_it | 2.187 |
r_symmetry_vdw_refined | 0.316 |
r_symmetry_hbond_refined | 0.288 |
r_nbd_refined | 0.234 |
r_xyhbond_nbd_refined | 0.168 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1921 |
Nucleic Acid Atoms | 2008 |
Solvent Atoms | 5 |
Heterogen Atoms | 17 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |