3DMD
Structures and Conformations in Solution of the Signal Recognition Particle Receptor from the archaeon Pyrococcus furiosus
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3DM9 | PDB ENTRY 3DM9 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5 | 293 | 0.9-1.2M Lithium Sulfate, 0.4-0.6M Ammonium Sulfate, 100 mM Na Citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.1 | 60.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 149.956 | α = 90 |
b = 102.368 | β = 119.81 |
c = 101.766 | 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 | 80 | CCD | ADSC QUANTUM 210 | 2006-08-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | ALS | 8.3.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.21 | 88.4 | 98.8 | 0.074 | 0.074 | 8.9 | 3.5 | 65992 | 65992 | 1 | 43 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.21 | 2.33 | 97.1 | 0.766 | 0.766 | 1.4 | 3.1 | 9460 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 3DM9 | 2.21 | 65.06 | 1.34 | 65548 | 2000 | 98.1 | 0.191 | 0.189 | 0.242 | 3.1% OF RANDOMLY SELECTED REFLECTIONS | 42 |
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] | |
2.2675 | -2.9906 | 0.5839 | -3.0836 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 15.865 |
f_angle_d | 0.939 |
f_chiral_restr | 0.064 |
f_bond_d | 0.006 |
f_plane_restr | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7399 |
Nucleic Acid Atoms | |
Solvent Atoms | 469 |
Heterogen Atoms | 86 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
ELVES | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHENIX | phasing |