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Human CD73 (ecto 5'-nucleotidase) in complex with PSB12690 (an AOPCP derivative, compound 10 in publication) in the closed state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H2I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 Reservoir: 5 % (w/v) polyethylene glycol 6000, 0.1 M NaMES pH 5.5. Drop:
1 microL crystallization buffer + 1 microL of 3 mg/mL protein in 10 mM Tris pH 8.0, 100 microM ZnCl2 and 1 mM of compound. Cryo buffer: 25% PEG200, 0.1 M NaMES pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.64 53.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.451 α = 90 b = 98.343 β = 90 c = 233.75 γ = 90
Symmetry Space Group C 2 2 21
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 2015-06-18 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 2.5 48.12 99.7 0.349 0.375 0.137 0.992 5.2 7.3 22226 66.87
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 2.5 2.6 99.6 5.007 5.402 2.007 0.179 7.1
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 4h2i 2.5 48.12 22178 593 99.68 0.2369 0.2361 0.2654 0.2656 0.2908 RANDOM 96.91
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] 17.2808 -42.437 25.1562
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.38 t_omega_torsion 3.9 t_angle_deg 1.12 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.38 t_omega_torsion 3.9 t_angle_deg 1.12 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4040 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 44
Software Software Software Name Purpose XDS data reduction Aimless data scaling BUSTER refinement PDB_EXTRACT data extraction BUSTER phasing