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Crystal structure of dCK C4S-S74E mutant in complex with UDP and the dCKi1 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 0.9 M Sodium citrate, 60 mM HEPES, pH 7.5,
Crystal Properties Matthews coefficient Solvent content 2.18 43.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.625 α = 90 b = 68.625 β = 90 c = 120.809 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 PILATUS 6M 2018-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.97625 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 1.85 48.53 100 0.188 0.057 6.1 10.8 25420 27.41
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 98.9 2.05 0.6 0.6 11.3
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 1.85 48.53 24091 1267 99.86 0.2041 0.2025 0.2113 0.2339 0.2418 RANDOM 35.514
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] -0.87 -0.87 1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.241 r_dihedral_angle_4_deg 18.034 r_dihedral_angle_3_deg 14.147 r_dihedral_angle_1_deg 5.993 r_angle_refined_deg 1.573 r_angle_other_deg 1.348 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.241 r_dihedral_angle_4_deg 18.034 r_dihedral_angle_3_deg 14.147 r_dihedral_angle_1_deg 5.993 r_angle_refined_deg 1.573 r_angle_other_deg 1.348 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1907 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement xia2 data scaling PDB_EXTRACT data extraction xia2 data reduction PHASER phasing