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Crystal structure of human CD73 (ecto-5'-nucleotidase) in complex with the AMPCP analog PSB-17230 in the closed state (crystal form IV)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model 6xue
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 5 % PEG 200, 10 mM PSB-17230, 20 % PEG 3350, 10 microM ZnCl2 and 0.1 M Tris pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.42 49.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.168 α = 90 b = 233.606 β = 90 c = 54.327 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 2018-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9793 PETRA III, EMBL c/o DESY P14 (MX2)
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 2.35 88.13 94.2 0.197 0.216 0.088 0.996 4.3 5.6 48282
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 2.35 2.43 46.5 1.719 2.059 1.098 0.425 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 2.35 88.13 1.33 47223 2335 92.15 0.2691 0.2667 0.2675 0.3156 0.3192
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.759 f_angle_d 0.601 f_chiral_restr 0.045 f_plane_restr 0.005 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8176 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 80
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction autoBUSTER phasing