2WGZ
Crystal structure of alpha-1,3 galactosyltransferase (alpha3GT) in a complex with p-nitrophenyl-beta-galactoside (pNP-beta-Gal)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1K4V | PDB ENTRY 1K4V |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8 | 5% PEG 6000, 0.1M TRIS-HCL, PH 8.0 IN THE PRESENCE OF 10MM MNCL2 AND 10MM UDP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.9 | 43 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 45.146 | ¦Á = 90 |
b = 94.222 | ¦Â = 99.05 |
c = 94.465 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 1 21 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 | MIRRORS | 2006-10-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SRS BEAMLINE PX14.1 | SRS | PX14.1 |
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 | 2.12 | 50 | 94.4 | 0.09 | 12.4 | 3.1 | 44578 | 22.9 |
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 | 2.12 | 2.2 | 80.7 | 0.22 | 5.14 | 3 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 1K4V | 2.12 | 25.29 | 40981 | 1077 | 94.6 | 0.16959 | 0.16865 | 0.20582 | RANDOM | 18.96 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.23 |
r_dihedral_angle_4_deg | 16.659 |
r_dihedral_angle_3_deg | 13.525 |
r_dihedral_angle_1_deg | 5.749 |
r_angle_other_deg | 1.481 |
r_scangle_it | 1.435 |
r_angle_refined_deg | 1.001 |
r_scbond_it | 0.885 |
r_mcangle_it | 0.649 |
r_mcbond_it | 0.372 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4784 |
Nucleic Acid Atoms | |
Solvent Atoms | 549 |
Heterogen Atoms | 130 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |