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Human Ecto-5'-nucleotidase (CD73) in complex with the AMPCP derivative A894 (compound 2n in publication) in the closed form (crystal form IV)
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 1mM of compound, 0.1 mM ZnCl2, 11-14% PEG6000, 100 mM sodium citrate pH 5.4-5.6, 15% glycerol for cryo
Crystal Properties Matthews coefficient Solvent content 2.45 49.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.03 α = 90 b = 232.12 β = 90 c = 53.79 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 2016-06-23 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 2.66 46.52 99.6 0.253 0.275 0.991 6.99 6.531 34420 45.71
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 2.66 2.82 98.9 0.867 0.943 0.487 1.95 6.515
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 2.66 46.52 34401 1721 99.4 0.197 0.193 0.214 0.268 0.2928 RANDOM 58.63
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] -3.5489 1.5439 2.0049
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.87 t_omega_torsion 3.04 t_angle_deg 1.22 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 20.87 t_omega_torsion 3.04 t_angle_deg 1.22 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 8153 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms 64
Software Software Software Name Purpose XSCALE data scaling BUSTER refinement PDB_EXTRACT data extraction XDS data reduction BUSTER phasing