4UDK
Crystal structure of b-1,4-mannopyranosyl-chitobiose phosphorylase at 1.76 Angstrom from unknown human gut bacteria (Uhgb_MP) in complex with N-acetyl-D-glucosamine, beta-D-mannopyranose and inorganic phosphate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7 | PROTEIN WAS CRYSTALLIZED FROM 17.5% PEG 3350, 200 MM NH4CL, pH 7.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.11 | 41.75 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 83.737 | α = 90 |
b = 140.886 | β = 90 |
c = 168.831 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | PAIR OF KB MIRRORS FOR ADJUSTABLE FOCUSING | 2014-09-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALBA BEAMLINE XALOC | ALBA | XALOC |
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 | 1.76 | 45 | 99.6 | 0.13 | 13.7 | 9.2 | 197652 | -1 |
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 | 1.76 | 1.86 | 97.8 | 0.92 | 2.54 | 8.9 |
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 4UDI | 1.76 | 108.17 | 187696 | 9956 | 99.59 | 0.15995 | 0.15823 | 0.1922 | RANDOM | 20.95 |
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] | |
0.21 | -1.05 | 0.85 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 27.589 |
r_dihedral_angle_4_deg | 12.957 |
r_dihedral_angle_3_deg | 12.467 |
r_dihedral_angle_1_deg | 7.045 |
r_scbond_it | 2.073 |
r_angle_refined_deg | 1.924 |
r_mcangle_it | 1.918 |
r_mcbond_it | 1.323 |
r_mcbond_other | 1.323 |
r_angle_other_deg | 0.915 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 15385 |
Nucleic Acid Atoms | |
Solvent Atoms | 1204 |
Heterogen Atoms | 260 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |