5YNV
Crystal structure of an aromatic prenyltransferase FAMD1 from Fischerella ambigua UTEX 1903 in complex with DMASPP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 295 | 1.0 M sodium citrate, 0.1 M Imidazole pH 8.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.81 | 56.26 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 93.917 | α = 90 |
b = 211.42 | β = 90 |
c = 82.52 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 | CCD | RAYONIX MX-300 | 2017-09-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSRRC BEAMLINE BL15A1 | 1.0 | NSRRC | BL15A1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.7 | 50 | 99.9 | 0.052 | 0.058 | 0.027 | 15.3 | 4.9 | 90773 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.7 | 1.76 | 99.7 | 0.336 | 0.378 | 0.172 | 0.924 | 4.8 |
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 | SIRAS | THROUGHOUT | 1.7 | 25 | 85679 | 4670 | 99.94 | 0.1177 | 0.1148 | 0.1709 | RANDOM | 26.238 |
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] | |
0.81 | -0.51 | -0.31 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.982 |
r_sphericity_free | 30.101 |
r_sphericity_bonded | 21.872 |
r_dihedral_angle_4_deg | 17.104 |
r_dihedral_angle_3_deg | 14.987 |
r_rigid_bond_restr | 8.708 |
r_dihedral_angle_1_deg | 6.736 |
r_angle_refined_deg | 1.45 |
r_chiral_restr | 0.121 |
r_gen_planes_refined | 0.018 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4901 |
Nucleic Acid Atoms | |
Solvent Atoms | 747 |
Heterogen Atoms | 34 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
SOLVE | phasing |