4UPI
Dimeric sulfatase SpAS1 from Silicibacter pomeroyi
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1E2S | PDB ENTRIES 1E2S, 2VQR, 1FSU, 1P49, 1HTH AS AN ENSEMBLE |
experimental model | PDB | 2VQR | PDB ENTRIES 1E2S, 2VQR, 1FSU, 1P49, 1HTH AS AN ENSEMBLE |
experimental model | PDB | 1FSU | PDB ENTRIES 1E2S, 2VQR, 1FSU, 1P49, 1HTH AS AN ENSEMBLE |
experimental model | PDB | 1P49 | PDB ENTRIES 1E2S, 2VQR, 1FSU, 1P49, 1HTH AS AN ENSEMBLE |
experimental model | PDB | 1HTH | PDB ENTRIES 1E2S, 2VQR, 1FSU, 1P49, 1HTH AS AN ENSEMBLE |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 0.1 M TRIS-HCL PH 8.0, 20% (W/V) PEG 6000, 0.75 M LICL |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.3 | 46.51 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 93.027 | α = 90 |
b = 86.029 | β = 115.19 |
c = 82.874 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 CCD | 2007-10-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
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 | 1.25 | 74.99 | 98.4 | 0.04 | 15.97 | 3.8 | 160317 | 2 | 23.378 |
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 | 1.25 | 1.28 | 89.1 | 0.51 | 2.2 | 2.87 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution 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 | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB ENTRIES 1E2S, 2VQR, 1FSU, 1P49, 1HTH AS AN ENSEMBLE | 1.25 | 37.497 | 1.36 | 160242 | 8048 | 98.5 | 0.1424 | 0.1413 | 0.1631 | 26.02 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 13.508 |
f_angle_d | 1.123 |
f_chiral_restr | 0.078 |
f_plane_restr | 0.006 |
f_bond_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4395 |
Nucleic Acid Atoms | |
Solvent Atoms | 768 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |