5ANN
Structure of fructofuranosidase from Xanthophyllomyces dendrorhous
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3LDK | PDB ENTRY 3LDK |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | PROTEIN WAS CRYSTALLIZED FROM 1.3M SODIUM CITRATE TRIBASIC DIHYDRATE, 0.1M HEPES PH 7.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.07 | 40.67 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 74.62 | ¦Á = 90 |
b = 205.18 | ¦Â = 90 |
c = 145.77 | ¦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 | CCD | ADSC QUANTUM 315r | MIRRORS | 2010-06-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | ESRF | ID23-1 |
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 | 2.14 | 61.92 | 99.9 | 0.11 | 12.8 | 7.1 | 117631 |
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 | 2.14 | 2.26 | 99.9 | 0.39 | 4.3 | 6.8 |
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 3LDK | 2.14 | 145.77 | 117374 | 6195 | 99.9 | 0.16995 | 0.16901 | 0.1879 | RANDOM | 21.193 |
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] | |
1.06 | -2.12 | 1.06 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.472 |
r_dihedral_angle_4_deg | 18.776 |
r_dihedral_angle_3_deg | 12.228 |
r_dihedral_angle_1_deg | 6.821 |
r_mcangle_it | 1.527 |
r_scbond_it | 1.412 |
r_angle_refined_deg | 1.372 |
r_mcbond_it | 0.861 |
r_chiral_restr | 0.08 |
r_bond_refined_d | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9594 |
Nucleic Acid Atoms | |
Solvent Atoms | 1217 |
Heterogen Atoms | 820 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
Aimless | data scaling |
MOLREP | phasing |