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Crystal structure of CD73 in complex with 4-nitrocatechol 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 100 mM 4-nitrocatechol. 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 49.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.21 α = 90 b = 131.645 β = 90 c = 66.348 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 2015-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 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 1.13 47.03 99.5 0.075 0.082 0.032 0.999 11.4 6.5 215998
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 1.13 1.15 90.2 1.079 1.179 0.468 0.577 6
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 1.13 46.77 205276 10623 99.48 0.1292 0.1283 0.1272 0.1454 0.144 RANDOM 14.312
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] -0.89 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.025 r_dihedral_angle_4_deg 18.433 r_dihedral_angle_3_deg 11.578 r_dihedral_angle_1_deg 9.121 r_rigid_bond_restr 5.501 r_angle_refined_deg 1.758 r_angle_other_deg 1.564 r_chiral_restr 0.099 r_bond_refined_d 0.013 r_gen_planes_refined 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.025 r_dihedral_angle_4_deg 18.433 r_dihedral_angle_3_deg 11.578 r_dihedral_angle_1_deg 9.121 r_rigid_bond_restr 5.501 r_angle_refined_deg 1.758 r_angle_other_deg 1.564 r_chiral_restr 0.099 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4026 Nucleic Acid Atoms Solvent Atoms 497 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing