7ZI8
Crystal structure of dCK C4S-S74E mutant in complex with UDP and the OR0602 inhibitor
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4KCG |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 285 | 0.9 M Sodium citrate, 60 mM HEPES |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.18 | 43.63 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68.618 | α = 90 |
b = 68.618 | β = 90 |
c = 121.247 | γ = 90 |
Symmetry | |
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Space Group | P 41 2 2 |
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 | 2020-09-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 2 | 0.980112 | SOLEIL | PROXIMA 2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.99 | 48.52 | 99.9 | 0.118 | 0.12 | 0.999 | 18.99 | 25.493 | 20446 | 58.247 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.99 | 2.11 | 99.3 | 3.387 | 3.459 | 0.41 | 0.87 | 24.524 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 4KCG | 1.99 | 48.52 | 19423 | 1023 | 99.88 | 0.2044 | 0.2014 | 0.2634 | RANDOM | 54.954 |
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] | |
-0.33 | -0.33 | 0.67 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.123 |
r_dihedral_angle_4_deg | 17.729 |
r_dihedral_angle_3_deg | 16.084 |
r_dihedral_angle_1_deg | 6.458 |
r_angle_refined_deg | 1.533 |
r_angle_other_deg | 1.328 |
r_chiral_restr | 0.076 |
r_bond_refined_d | 0.008 |
r_gen_planes_refined | 0.008 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1915 |
Nucleic Acid Atoms | |
Solvent Atoms | 32 |
Heterogen Atoms | 65 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
PHASER | phasing |