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Human Ecto-5'-nucleotidase (CD73) in complex with AOPCP derivative A830 (compound 16 in publication) in the closed form (crystal form III)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H2I pdbid 4H2I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 CD73 at 7 mg/mL was incubated on ice for one hour with 1mM of the inhibitor and 0.1 mM ZnCl2. 1 uL of protein was mixed with 1 uL of 11-14% PEG6000 and 100 mM sodium citrate pH 5.4-5.6. For cryoprotection glycerol was added to a final concentration of 15 % to the reservoir buffer.
Crystal Properties Matthews coefficient Solvent content 2.55 51.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.24 α = 90 b = 96.45 β = 90 c = 235.17 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 2016-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91840 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 2.17 48.23 99.2 0.223 0.243 0.99 8.61 6.425 32496 32.78
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 2.17 2.3 96.4 0.836 0.915 0.837 1.8 6.038
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 pdbid 4H2I 2.17 48.23 32496 1625 99.2 0.21 0.208 0.2193 0.263 0.2766 RANDOM 42.75
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] 2.532 -13.9648 11.4328
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.13 t_omega_torsion 3.48 t_angle_deg 1.16 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 20.13 t_omega_torsion 3.48 t_angle_deg 1.16 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_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4064 Nucleic Acid Atoms Solvent Atoms 285 Heterogen Atoms 38
Software Software Software Name Purpose XSCALE data scaling BUSTER refinement PDB_EXTRACT data extraction XDS data reduction BUSTER phasing