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Crystal structure of CD73 in complex with 5-iodouracil in the open form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H2G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 7 mg/mL protein concentration, 100 mM Tris pH 7.8, 10 % PEG6000, equal amounts of protein and reservoir. Following crystal formation (1-2 days), the crystals were transferred to soaking solution containing reservoir solution and 10 mM 5-iodouracil. Crystals were then transferred to cryo solution containing an additional 20 % glycerol, soaked for ~2-5 min, and flash frozen in liquid nitrogen.
Crystal Properties Matthews coefficient Solvent content 2.43 49.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.22 α = 90 b = 131.82 β = 90 c = 66.324 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 2017-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.377 47.26 99.1 0.054 0.999 11.3 3.7 122396
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.377 1.4 0.768 0.534 1.4
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 FOURIER SYNTHESIS THROUGHOUT 4h2g 1.377 47.26 114949 6109 98.91 0.1272 0.1251 0.1243 0.1664 0.1663 RANDOM 17.283
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] -0.58 -0.11 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.409 r_dihedral_angle_4_deg 16.855 r_dihedral_angle_3_deg 11.924 r_dihedral_angle_1_deg 9.041 r_rigid_bond_restr 3.353 r_angle_refined_deg 1.873 r_angle_other_deg 1.538 r_chiral_restr 0.105 r_bond_refined_d 0.014 r_gen_planes_refined 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.409 r_dihedral_angle_4_deg 16.855 r_dihedral_angle_3_deg 11.924 r_dihedral_angle_1_deg 9.041 r_rigid_bond_restr 3.353 r_angle_refined_deg 1.873 r_angle_other_deg 1.538 r_chiral_restr 0.105 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4076 Nucleic Acid Atoms Solvent Atoms 479 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling REFMAC phasing