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Crystal structure of dCK C4S-S74E mutant in complex with UDP and the OR0642 inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KCG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 285 0.9 M Sodium citrate, 60 mM HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.19 43.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.94 α = 90 b = 68.94 β = 90 c = 120.763 γ = 90
Symmetry Space Group P 41 2 2
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 16M 2021-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.978566 SOLEIL PROXIMA 1
Data Collection Overall 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 1.9 48.75 99.9 0.085 0.086 0.999 19.73 25.766 23515 54.889
Highest Resolution Shell 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 1.9 2.02 99.8 2.593 2.642 0.626 1.12 26.927
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 4KCG 1.9 48.75 22339 1176 99.94 0.1917 0.1896 0.1995 0.2303 0.2357 RANDOM 51.899
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] -0.33 -0.33 0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.618 r_dihedral_angle_3_deg 16.693 r_dihedral_angle_4_deg 15.518 r_dihedral_angle_1_deg 6.611 r_angle_refined_deg 1.601 r_angle_other_deg 1.369 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.618 r_dihedral_angle_3_deg 16.693 r_dihedral_angle_4_deg 15.518 r_dihedral_angle_1_deg 6.611 r_angle_refined_deg 1.601 r_angle_other_deg 1.369 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1923 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement XDS data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing