8B7U
Bacterial chalcone isomerase H33A with taxifolin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4D06 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | 6.8 mg/ml CHI 50 mM Na phosphate, pH 6.8. Precipitant 1.5 M (NH4)2SO4, 0.2 M NaCl, 0.1 M HEPES pH 7.5. Hanging drop 2+2 ul. soaking for 10 min in 2.5 mM taxifolin (2.5% ethanol) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.95 | 75.16 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 187.582 | α = 90 |
b = 203.736 | β = 90 |
c = 560.388 | γ = 90 |
Symmetry | |
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Space Group | I 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 | 2016-11-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.9184 | BESSY | 14.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | 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 | 2.78 | 49.423 | 99.3 | 0.368 | 0.99 | 9.3 | 13.7 | 266311 | 42.4 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.78 | 2.95 | 98.2 | 1.58 | 0.24 | 1.76 | 13.3 |
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 (All) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 4D06 | 2.8 | 49.423 | 260531 | 2736 | 99.448 | 0.214 | 0.2134 | 0.22 | 0.2245 | 0.23 | 66.89 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
0.431 | -0.232 | -0.199 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_6_deg | 15.628 |
r_dihedral_angle_3_deg | 15.021 |
r_dihedral_angle_2_deg | 9.205 |
r_dihedral_angle_1_deg | 8.01 |
r_lrange_it | 7.95 |
r_lrange_other | 7.95 |
r_scangle_it | 2.787 |
r_scangle_other | 2.675 |
r_scbond_it | 1.991 |
r_scbond_other | 1.876 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 38176 |
Nucleic Acid Atoms | |
Solvent Atoms | 128 |
Heterogen Atoms | 875 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |