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Crystal structure of Yck2 with LY364947
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 7.5 298 0.1 M Tris pH 8, 25 mM Magnesium chloride, 20% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.71 54.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.532 α = 90 b = 91.532 β = 90 c = 118.824 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 R 1M 2024-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU MICROMAX-003 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 29.95 99.8 0.05 0.999 19.25 3.4 40815 26.51
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 98.8 0.622 0.445 0.48 1.7
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.7 29.95 1.96 40743 1949 99.68 0.1761 0.1743 0.1743 0.2111 0.2112 39.97
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 14.4664 f_angle_d 1.1119 f_chiral_restr 0.0742 f_bond_d 0.0111 f_plane_restr 0.0096
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2469 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms 23
Software Software Software Name Purpose PHENIX refinement CrysalisPro data reduction CrysalisPro data scaling PHASER phasing PHENIX model building Coot model building