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Crystal structure of dCK C4S-S74E mutant in complex with UDP and the OR0635 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 7.5 285 1 M Sodium citrate, 67 mM HEPES
Crystal Properties Matthews coefficient Solvent content 2.16 43.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.506 α = 90 b = 68.506 β = 90 c = 120.334 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 PILATUS3 2M 2021-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965459 ESRF MASSIF-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 1.93 45.21 99.8 0.077 0.082 0.999 16.12 9.386 22140 45.345
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 1.93 2.05 99.7 1.27 1.35 0.565 1.5 9.264
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 1.95 45.21 20501 1079 99.83 0.1809 0.1783 0.1889 0.232 0.2366 RANDOM 42.052
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] 0.16 0.16 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.926 r_dihedral_angle_3_deg 16.356 r_dihedral_angle_4_deg 16.267 r_dihedral_angle_1_deg 6.415 r_angle_refined_deg 1.648 r_angle_other_deg 1.385 r_chiral_restr 0.075 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.926 r_dihedral_angle_3_deg 16.356 r_dihedral_angle_4_deg 16.267 r_dihedral_angle_1_deg 6.415 r_angle_refined_deg 1.648 r_angle_other_deg 1.385 r_chiral_restr 0.075 r_bond_refined_d 0.011 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 1908 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement XDS data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing