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Crystal structure of Yck2 from Candida albicans in complex with inhibitor 1f: 7-fluoro-2-(4-fluorophenyl)-3-(pyridin-4-yl)imidazo[1,2-a]pyridine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6U6A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 0.1 M Tris pH 8, 25 mM Magnesium chloride, 20% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.73 54.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.175 α = 90 b = 92.175 β = 90 c = 118.199 γ = 120
Diffraction Diffraction Experiment 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 2024-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1.18077 CLSI 08B1-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 2.33 66.14 99.9 0.094 0.05 0.98 8 8.9 15999 45.67
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.33 2.39 100 2.113 1.277 0.265 0.9 7.4
Refinement Statistics 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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.33 66.14 1.96 15954 822 99.66 0.2703 0.269 0.2647 0.2904 0.2874 RANDOM 98.91
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.1127 f_angle_d 0.5533 f_chiral_restr 0.0413 f_plane_restr 0.0043 f_bond_d 0.0026
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2469 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 24
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling PHENIX phasing