4BL5
Crystal structure of human GDP-L-fucose synthase with bound NADP and product GDP-L-fucose
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4B8W | PDB ENTRY 4B8W |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 0.1M BIS-TRIS-PROPANE PH 7.5, 0.15M SODIUM CHLORIDE, 25% PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.17 | 43.36 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 90.407 | ¦Á = 72.54 |
b = 90.478 | ¦Â = 72.64 |
c = 147.518 | ¦Ã = 60.14 |
Symmetry | |
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Space Group | P 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 | DECTRIS PILATUS 6M | 2012-09-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | Diamond | I04 |
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 | 2.6 | 29.64 | 97.4 | 0.14 | 61.2 | 2.1 | 113998 | 3.3 | 42.5 |
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 | 2.6 | 2.64 | 78.1 | 1.15 | 3.3 | 2.1 |
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 4B8W | 2.6 | 29.66 | 107442 | 5653 | 96.68 | 0.22482 | 0.22163 | 0.28565 | RANDOM | 45.598 |
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] | |
-0.71 | 0.2 | -0.37 | 0.27 | -0.3 | 0.21 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.711 |
r_dihedral_angle_4_deg | 16.524 |
r_dihedral_angle_3_deg | 15.449 |
r_dihedral_angle_1_deg | 6.553 |
r_mcangle_it | 2.338 |
r_mcbond_it | 1.43 |
r_mcbond_other | 1.43 |
r_angle_refined_deg | 1.38 |
r_scbond_it | 1.324 |
r_angle_other_deg | 0.816 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 28839 |
Nucleic Acid Atoms | |
Solvent Atoms | 41 |
Heterogen Atoms | 1036 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |