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Crystal structure of CD73 in complex with UMP 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 UMP. 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 2.42 49.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.227 α = 90 b = 131.648 β = 90 c = 66.173 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 CCD RAYONIX MX-225 2016-10-04 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) 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 1.28 47.2 98.6 0.08 0.092 0.045 0.997 10.3 4 148582
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 1.28 1.3 84.8 0.652 0.791 0.438 0.591 2.8
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 1.28 47.2 141079 7461 98.46 0.1278 0.1263 0.1258 0.1578 0.158 RANDOM 13.373
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] -0.47 1.43 -0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.634 r_dihedral_angle_4_deg 18.187 r_dihedral_angle_3_deg 11.251 r_dihedral_angle_1_deg 9.251 r_rigid_bond_restr 3.424 r_angle_refined_deg 1.95 r_angle_other_deg 1.589 r_chiral_restr 0.121 r_bond_refined_d 0.016 r_gen_planes_refined 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.634 r_dihedral_angle_4_deg 18.187 r_dihedral_angle_3_deg 11.251 r_dihedral_angle_1_deg 9.251 r_rigid_bond_restr 3.424 r_angle_refined_deg 1.95 r_angle_other_deg 1.589 r_chiral_restr 0.121 r_bond_refined_d 0.016 r_gen_planes_refined 0.013 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4047 Nucleic Acid Atoms Solvent Atoms 469 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing