8JRD
Chalcone synthase from Glycine max (L.) Merr (soybean) complexed with naringenin and coenzyme A
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7BUS |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 293 | 30% PEG 4000, 0.2 M ammonium acetate, 0.1M sodium citrate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.35 | 47.61 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 54.61 | α = 90 |
b = 97.47 | β = 90 |
c = 157.54 | γ = 90 |
Symmetry | |
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Space Group | P 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 EIGER X 9M | 2020-11-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL32XU | 1.00000 | SPring-8 | BL32XU |
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 | 1.83 | 50 | 100 | 0.22 | 0.997 | 12.94 | 15.66 | 75109 |
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 | 1.83 | 1.94 | 100 | 1.33 | 0.745 | 2.29 | 12.3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.83 | 48.78 | 71283 | 3744 | 99.99 | 0.15194 | 0.1502 | 0.18514 | RANDOM | 22.515 |
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] | |
-0.63 | 0.28 | 0.34 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.727 |
r_dihedral_angle_4_deg | 17.665 |
r_dihedral_angle_3_deg | 13.969 |
r_long_range_B_refined | 6.974 |
r_long_range_B_other | 6.838 |
r_dihedral_angle_1_deg | 6.552 |
r_scangle_other | 5.419 |
r_scbond_it | 3.636 |
r_scbond_other | 3.636 |
r_mcangle_other | 2.332 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5988 |
Nucleic Acid Atoms | |
Solvent Atoms | 703 |
Heterogen Atoms | 207 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DIALS | data reduction |
XDS | data reduction |
XSCALE | data scaling |
MOLREP | phasing |