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Crystal structure of Yck2 from Candida albicans in complex with inhibitor 2b: 6-fluoro-2-(4-fluorophenyl)-3-(pyridin-4-yl)pyrazolo[1,5-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, 0.025 M Magnesium chloride, 20% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.69 54.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.488 α = 90 b = 91.488 β = 90 c = 119.17 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 2023-04-13 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 2.3 47.64 99.9 0.117 0.09 0.988 5.3 4.5 16511 58.56
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 2.3 2.36 99.2 1.341 1.138 0.321 0.7 3.3
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 2.3 47.62 1.96 16481 976 99.61 0.2046 0.2024 0.2027 0.2376 0.2383 RANDOM 69.54
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 14.3578 f_angle_d 0.4762 f_chiral_restr 0.0379 f_plane_restr 0.0039 f_bond_d 0.0021
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2460 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 26
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling PHENIX phasing