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Crystal structure of human uridine-cytidine kinase 2 complexed with a weak small molecule inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UFQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 293 4% glycerol, 100 mM HEPES pH 6.9, 8% PEG 3350, and 30% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.76 55.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.087 α = 90 b = 93.893 β = 90 c = 157.497 γ = 90
Symmetry Space Group P 21 21 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 Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2 2020-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.4 39.7 99.6 0.233 0.245 0.073 0.995 11.4 11.9 49319
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.48 99.3 3.004 3.163 0.972 0.457 11.2
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 1UFQ 2.4 39.7 46673 2414 98.98 0.2025 0.1997 0.2045 0.2566 0.2573 RANDOM 48.388
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] 1.07 -1.25 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.062 r_dihedral_angle_4_deg 19.377 r_dihedral_angle_3_deg 17.993 r_dihedral_angle_1_deg 7.151 r_angle_refined_deg 1.503 r_angle_other_deg 1.215 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.062 r_dihedral_angle_4_deg 19.377 r_dihedral_angle_3_deg 17.993 r_dihedral_angle_1_deg 7.151 r_angle_refined_deg 1.503 r_angle_other_deg 1.215 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6788 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 236
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction