5FKB
Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with 1-Kestose
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5ANN | PDB ENTRY 5ANN |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8.5 | PROTEIN WAS CRYSTALLIZED FROM 1.2M SODIUM CITRATE TRIBASIC DIHYDRATE, 0.1M TRIS-HCL PH 8.5, THEN SOAKED IN 30MM 1-KESTOSE |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.08 | 70.7 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 74.526 | ¦Á = 90 |
b = 205.019 | ¦Â = 90 |
c = 145.988 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 | MIRRORS | 2014-01-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) | 0.9786 | PETRA III, EMBL c/o DESY | P13 (MX1) |
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 | 1.78 | 118.92 | 99.9 | 0.06 | 19.5 | 6.7 | 213888 |
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 | 1.78 | 1.81 | 99.8 | 0.53 | 3.3 | 6.8 |
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 5ANN | 1.78 | 118.92 | 203088 | 10689 | 99.89 | 0.17109 | 0.1704 | 0.18414 | RANDOM | 26.572 |
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] | |
1.49 | -2.54 | 1.05 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.501 |
r_dihedral_angle_4_deg | 17.872 |
r_dihedral_angle_3_deg | 10.211 |
r_dihedral_angle_1_deg | 6.755 |
r_scangle_it | 2.669 |
r_scbond_it | 1.637 |
r_angle_refined_deg | 1.402 |
r_mcangle_it | 1.398 |
r_angle_other_deg | 1.091 |
r_mcbond_it | 0.911 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9588 |
Nucleic Acid Atoms | |
Solvent Atoms | 1641 |
Heterogen Atoms | 889 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |