7L4A
Crystal Structure of Cytidylate kinase from Encephalitozoon cuniculi GB-M1 in complex with two CDP molecules
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 21-ID-F |
Synchrotron site | APS |
Beamline | 21-ID-F |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2020-12-03 |
Detector | RAYONIX MX-300 |
Wavelength(s) | 0.97872 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 48.520, 46.870, 53.830 |
Unit cell angles | 90.00, 112.59, 90.00 |
Refinement procedure
Resolution | 44.800 - 1.500 |
R-factor | 0.1507 |
Rwork | 0.148 |
R-free | 0.19030 |
Structure solution method | SAD |
RMSD bond length | 0.008 |
RMSD bond angle | 0.954 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHASER |
Refinement software | PHENIX (1.19rc4 4035) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 1.540 |
High resolution limit [Å] | 1.500 | 6.710 | 1.500 |
Rmerge | 0.042 | 0.026 | 0.448 |
Rmeas | 0.049 | 0.031 | 0.538 |
Number of reflections | 35784 | 425 | 2562 |
<I/σ(I)> | 17.71 | 39.97 | 2.49 |
Completeness [%] | 99.5 | 98.2 | 97 |
Redundancy | 4.026 | 3.732 | 3.189 |
CC(1/2) | 0.999 | 0.998 | 0.822 |
Crystallization Conditions
crystal 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. |
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. |