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Human CD73 (ecto 5'-nucleotidase) in complex with compound 21
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Proprietary model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 SPG buffer 0.1M pH4.0, 15% Peg 1500
Crystal Properties Matthews coefficient Solvent content 2.52 51.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 230.585 α = 90 b = 94.048 β = 90 c = 54.86 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 2019-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00006 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.43 115.29 96 0.078 0.998 11.58 2.8 44168
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.43 2.68 98.4 0.448 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MOLECULAR REPLACEMENT THROUGHOUT 2.43 115.29 43064 1104 95.98 0.21164 0.21063 0.214 0.25078 0.2531 RANDOM 57.061
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] -4.96 5.78 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.523 r_dihedral_angle_4_deg 15.46 r_dihedral_angle_3_deg 13.133 r_long_range_B_refined 7.101 r_dihedral_angle_1_deg 7.097 r_long_range_B_other 7.082 r_scangle_other 4.831 r_mcangle_it 3.912 r_mcangle_other 3.912 r_scbond_it 3.394
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.523 r_dihedral_angle_4_deg 15.46 r_dihedral_angle_3_deg 13.133 r_long_range_B_refined 7.101 r_dihedral_angle_1_deg 7.097 r_long_range_B_other 7.082 r_scangle_other 4.831 r_mcangle_it 3.912 r_mcangle_other 3.912 r_scbond_it 3.394 r_scbond_other 3.279 r_mcbond_it 2.584 r_mcbond_other 2.581 r_angle_refined_deg 1.576 r_angle_other_deg 1.277 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8214 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 130
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement REFMAC phasing PDB_EXTRACT data extraction