4C5Y
Crystal structure of A. niger ochratoxinase
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3BE7 | PDB ENTRIES 3BE7, 3FEQ, 2R8C, 3MTW, 2QS8 |
experimental model | PDB | 3FEQ | PDB ENTRIES 3BE7, 3FEQ, 2R8C, 3MTW, 2QS8 |
experimental model | PDB | 2R8C | PDB ENTRIES 3BE7, 3FEQ, 2R8C, 3MTW, 2QS8 |
experimental model | PDB | 3MTW | PDB ENTRIES 3BE7, 3FEQ, 2R8C, 3MTW, 2QS8 |
experimental model | PDB | 2QS8 | PDB ENTRIES 3BE7, 3FEQ, 2R8C, 3MTW, 2QS8 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 9 | 12% (W/V) PEG 3000, 0.1 M BICINE PH 9.0, 0.2 M TRI-POTASSIUM CITRATE |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.56 | 65.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 183.24 | α = 90 |
b = 183.24 | β = 90 |
c = 78.98 | γ = 90 |
Symmetry | |
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Space Group | P 4 21 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 | PIXEL | DECTRIS PILATUS 6M | 2011-07-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | ESRF | ID29 |
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 | 3 | 72.5 | 96.2 | 0.2 | 6.3 | 5.5 | 26324 |
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 | 3 | 3.16 | 97.2 | 0.75 | 2.2 | 5.7 |
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 ENTRIES 3BE7, 3FEQ, 2R8C, 3MTW, 2QS8 | 3 | 67.44 | 24926 | 1341 | 95.39 | 0.18999 | 0.18801 | 0.22583 | RANDOM | 59.349 |
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] | |
-1.55 | -1.55 | 3.11 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.079 |
r_dihedral_angle_4_deg | 17.746 |
r_dihedral_angle_3_deg | 17.607 |
r_dihedral_angle_1_deg | 6.223 |
r_long_range_B_refined | 5.385 |
r_long_range_B_other | 5.383 |
r_scangle_other | 2.768 |
r_mcangle_it | 2.529 |
r_mcangle_other | 2.529 |
r_scbond_it | 1.737 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6516 |
Nucleic Acid Atoms | |
Solvent Atoms | 31 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
iMOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |