2YDT
STRUCTURE OF THE ALPHA-L-ARABINOFURANOSIDASE ARB93A from FUSARIUM Graminearum in complexe with an iminosugar inhibitor
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 2W5N | PDB ENTRY 2W5N |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 7.5 | 38% PEG 550MME, 100 MM HEPES PH 7.5, 100 MM MNSO4. |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.37 | 48.07 |
Crystal Data
Unit Cell | |
---|---|
Length ( ? ) | Angle ( ? ) |
a = 105.435 | ¦Á = 90 |
b = 105.435 | ¦Â = 90 |
c = 140.038 | ¦Ã = 90 |
Symmetry | |
---|---|
Space Group | I 41 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC CCD | 2010-07-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM30A | ESRF | BM30A |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 44.69 | 100 | 0.06 | 11 | 7.6 | 55107 | 2 |
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 | 1.67 | 99.8 | 0.38 | 2 | 5 |
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 2W5N | 1.6 | 44.69 | 49382 | 2656 | 99.9 | 0.144 | 0.142 | 0.17 | RANDOM | 9.74 |
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] | |
0.16 | 0.16 | -0.33 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.881 |
r_dihedral_angle_4_deg | 13.312 |
r_dihedral_angle_3_deg | 12.405 |
r_dihedral_angle_1_deg | 7.279 |
r_scangle_it | 3.356 |
r_scbond_it | 2.141 |
r_angle_refined_deg | 1.604 |
r_mcangle_it | 1.407 |
r_angle_other_deg | 0.937 |
r_mcbond_it | 0.84 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2848 |
Nucleic Acid Atoms | |
Solvent Atoms | 524 |
Heterogen Atoms | 52 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |