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Crystal structure of CD73 in complex with CMP 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 7.8 292 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 100 mM CMP. 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 2.45 49.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.569 α = 90 b = 131.676 β = 90 c = 66.493 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 2016-06-23 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 1.45 47.44 94.3 0.071 0.078 0.031 0.999 16.9 5.9 99435
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 1.45 1.48 64.7 0.629 0.771 0.428 0.6 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 FOURIER SYNTHESIS THROUGHOUT 4h2g 1.45 47.44 94400 4972 94.19 0.1207 0.1185 0.1184 0.1609 0.1606 RANDOM 13.781
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] -0.16 -0.4 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.33 r_dihedral_angle_4_deg 18.554 r_dihedral_angle_3_deg 11.98 r_dihedral_angle_1_deg 9.147 r_rigid_bond_restr 3.08 r_angle_refined_deg 1.914 r_angle_other_deg 1.57 r_chiral_restr 0.113 r_bond_refined_d 0.015 r_gen_planes_refined 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.33 r_dihedral_angle_4_deg 18.554 r_dihedral_angle_3_deg 11.98 r_dihedral_angle_1_deg 9.147 r_rigid_bond_restr 3.08 r_angle_refined_deg 1.914 r_angle_other_deg 1.57 r_chiral_restr 0.113 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4050 Nucleic Acid Atoms Solvent Atoms 533 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing