4UDG
Crystal structure of b-1,4-mannopyranosyl-chitobiose phosphorylase at 1.60 Angstrom in complex with N-acetylglucosamine and inorganic phosphate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1VKD | PDB ENTRY 1VKD |
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 | 41.74 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 83.816 | α = 90 |
b = 140.912 | β = 90 |
c = 168.598 | 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 | 1.6 | 47 | 99.9 | 0.1 | 14.49 | 9.37 | 261651 | -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 | 1.6 | 1.7 | 99.3 | 1.1 | 2.07 | 9.4 |
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 1VKD | 1.6 | 108.12 | 248496 | 13154 | 99.84 | 0.15507 | 0.15361 | 0.18297 | RANDOM | 22.301 |
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] | |
0.04 | -0.56 | 0.52 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 27.883 |
r_dihedral_angle_4_deg | 14.252 |
r_dihedral_angle_3_deg | 12.736 |
r_dihedral_angle_1_deg | 6.968 |
r_long_range_B_refined | 5.35 |
r_long_range_B_other | 5.347 |
r_scangle_other | 3.71 |
r_scbond_it | 2.479 |
r_scbond_other | 2.479 |
r_mcangle_it | 2.212 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 15410 |
Nucleic Acid Atoms | |
Solvent Atoms | 1463 |
Heterogen Atoms | 188 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |