1SYO
N-terminal 3 domains of CI-MPR bound to mannose 6-phosphate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1Q25 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 6.35 | 292 | 25% PEG 4000, 0.1M sodium cacodylate (pH 6.35), 150mM NaCl, 50 mM imidazole (pH 6.7), 10 mM manganese chloride, 5mM beta-glycerophosphate, 10 mM mannose 6-phosphate, vapor diffusion, sitting drop, temperature 292K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.26 | 45.1 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 61.4 | α = 90 |
b = 86.4 | β = 108.8 |
c = 86.9 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | 103 | IMAGE PLATE | RIGAKU RAXIS IIC | CONFOCAL BLUE | 2000-05-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 |
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 | 2.2 | 29.96 | 88.8 | 0.064 | 38820 | 12.7 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.2 | 2.28 | 55.8 | 0.301 |
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 (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 | 1Q25 | 2.2 | 29.96 | 1 | 42801 | 38615 | 2600 | 88.3 | 0.228 | 0.228 | 0.289 | RANDOM | 39.96 |
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] | |
-6.73 | 6.16 | -4.71 | 11.44 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_angle_deg | 1.4 |
c_bond_d | 0.007 |
c_bond_d_na | |
c_bond_d_prot | |
c_angle_d | |
c_angle_d_na | |
c_angle_d_prot | |
c_angle_deg_na | |
c_angle_deg_prot | |
c_dihedral_angle_d |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6429 |
Nucleic Acid Atoms | |
Solvent Atoms | 336 |
Heterogen Atoms | 126 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |
CNS | refinement |