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Human Ecto-5'-nucleotidase (CD73) in complex with A1618 (compound 1b in publication) in the closed state in crystal form III
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 8 291 Reservoir: 7.5 % PEG 6.000, 0.1 M MES pH 6.2. Drop: 1 micro-L crystallization buffer + 1 micro-L of 3 mg/mL CD73 in 10 mM Tris pH 8.0, 10 micro-M ZnCl2 and 1 mM of compound. Cryo: 20% PEG200 in crystallization drop
Crystal Properties Matthews coefficient Solvent content 2.38 48.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.09 α = 90 b = 93.85 β = 90 c = 235.66 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 2018-03-02 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) 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 1.97 47.13 99.6 0.12 0.142 0.998 6.81 3.482 80202 53.22
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2.09 99.2 3.381 3.984 0.135 0.37 3.528
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 4h2i 1.97 46.21 42108 1103 99.8 0.213 0.212 0.239 0.2446 RANDOM 67.82
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] -1.9834 -0.6547 2.6381
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.48 t_omega_torsion 3.49 t_angle_deg 1.19 t_bond_d 0.01 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 18.48 t_omega_torsion 3.49 t_angle_deg 1.19 t_bond_d 0.01 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_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3997 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 40
Software Software Software Name Purpose BUSTER refinement XDS data reduction XDS data scaling PDB_EXTRACT data extraction BUSTER phasing