7L4A
Crystal Structure of Cytidylate kinase from Encephalitozoon cuniculi GB-M1 in complex with two CDP molecules
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 287 | Optimization condition: 100mM BisTris pH 6, 200mM ammonium sulfate, 26% (w/V) PEG 3350: EucuA.01086.a.AE1.PS38633 at 56.56mg/ml + 5mM CTP + 5mM MgCl2: tray 318933 a2: cryo: 20% EG + ligands: puck akp1-5. For phasing, a crystal from MCSG1, condition D7 (20% (w/V) PEG 3000, 100mM sodium citrate tribasic / citric acid pH 5.5: EncuA.01086.a.AE1.PS38636 at 28.28mg/ml, tray 315976 d7) was dipped for 20sec in a solution of 4ul half saturated NaI in ethylene glycol and reservoir and directly vitrified. This crystal form could not be reproduced. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.15 | 42.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 48.52 | α = 90 |
b = 46.87 | β = 112.592 |
c = 53.83 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | Beryllium Lenses | 2020-12-03 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 100 | CCD | RIGAKU SATURN 944+ | 2020-07-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
2 | ROTATING ANODE | RIGAKU FR-E+ SUPERBRIGHT | 1.5418 |
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 | 1.5 | 50 | 99.5 | 0.042 | 0.049 | 0.999 | 17.71 | 4.026 | 35784 | 25.36 |
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) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.5 | 1.54 | 97 | 0.448 | 0.538 | 0.822 | 2.49 | 3.189 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | SAD | FREE R-VALUE | 1.5 | 44.8 | 1.36 | 35775 | 2003 | 99.64 | 0.1507 | 0.1482 | 0.1903 | 0 | 25.13 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 11.1348 |
f_angle_d | 0.9541 |
f_chiral_restr | 0.0586 |
f_plane_restr | 0.0118 |
f_bond_d | 0.0081 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1779 |
Nucleic Acid Atoms | |
Solvent Atoms | 235 |
Heterogen Atoms | 59 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
PHASER | phasing |
PARROT | phasing |
ARP/wARP | model building |
Coot | model building |