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Crystal structure of dCK C4S-S74E mutant in complex with EdC and UDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ZI3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 285 HEPES 70 mM pH 7.5
Sodium citrate 1.1 M
Crystal Properties Matthews coefficient Solvent content 2.13 42.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.47 α = 90 b = 138.389 β = 90 c = 116.825 γ = 90
Symmetry Space Group C 2 2 21
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 2022-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9785 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 48.76 99.8 0.999 9.64 14.99 65390
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.22 0.683
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.1 48.76 61833 3255 99.94 0.2388 0.23667 0.2402 0.27943 0.2824 RANDOM 54.444
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] -1.35 -3.43 4.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.051 r_long_range_B_other 7.278 r_long_range_B_refined 7.277 r_dihedral_angle_1_deg 6.279 r_scangle_other 4.744 r_mcangle_it 4.215 r_mcangle_other 4.215 r_dihedral_angle_2_deg 2.925 r_scbond_it 2.857 r_scbond_other 2.857
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.051 r_long_range_B_other 7.278 r_long_range_B_refined 7.277 r_dihedral_angle_1_deg 6.279 r_scangle_other 4.744 r_mcangle_it 4.215 r_mcangle_other 4.215 r_dihedral_angle_2_deg 2.925 r_scbond_it 2.857 r_scbond_other 2.857 r_mcbond_it 2.62 r_mcbond_other 2.619 r_angle_refined_deg 0.905 r_angle_other_deg 0.325 r_chiral_restr 0.046 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7768 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 172
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing