4V2U
Apo-structure of alpha2,3-sialyltransferase from Pasteurella dagmatis
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2ILV | PDB ENTRY 2ILV |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 3.3 MG/ML OF PROTEIN INDEX SCREEN CONDITION D9 (0.1M TRIS PH 8.5, 25% W/V POLYETHYLENE GLYCOL 3350) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.6 | 53 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 111.724 | ¦Á = 90 |
b = 56.59 | ¦Â = 111.95 |
c = 79.542 | ¦Ã = 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 | 100 | PIXEL | PILATUS | 2014-01-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, DESY BEAMLINE P11 | PETRA III, DESY | P11 |
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 | 2.71 | 45.1 | 98.8 | 0.11 | 10.4 | 3.3 | 12618 | 1.9 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.71 | 2.87 | 97.3 | 0.63 | 1.9 | 3.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 2ILV | 2.71 | 45.11 | 11987 | 631 | 99.03 | 0.19018 | 0.1863 | 0.26099 | RANDOM | 46.174 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.89 | 0.64 | -1.78 | 1.63 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.47 |
r_dihedral_angle_3_deg | 18.993 |
r_dihedral_angle_4_deg | 18.976 |
r_dihedral_angle_1_deg | 6.32 |
r_mcangle_it | 5.004 |
r_scbond_it | 3.598 |
r_mcbond_other | 3.248 |
r_mcbond_it | 3.247 |
r_angle_refined_deg | 1.646 |
r_angle_other_deg | 0.818 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3207 |
Nucleic Acid Atoms | |
Solvent Atoms | 11 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |