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Crystal structure of CD73 in complex with IMP in the open form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H2G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 7 mg/mL protein concentration, 100 mM Tris pH 7.8, 10 % PEG6000, equal amounts of protein and reservoir. Following crystal formation (1-2 days), the crystals were transferred to soaking solution containing reservoir solution and 25 mM IMP. Crystals were then transferred to cryo solution containing an additional 20 % glycerol, soaked for ~2-5 min, and flash frozen in liquid nitrogen.
Crystal Properties Matthews coefficient Solvent content 2.46 49.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.711 α = 90 b = 131.852 β = 90 c = 66.634 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 2016-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 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 1.42 47.49 99.3 0.079 0.086 0.034 0.999 15.9 6.3 111168
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 1.42 1.45 88.6 0.828 0.964 0.477 0.567 3.6
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 4h2g 1.42 44.72 105543 5562 99.25 0.1296 0.1275 0.1274 0.1682 0.1685 RANDOM 13.159
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] 0.74 -0.47 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.195 r_dihedral_angle_4_deg 16.701 r_dihedral_angle_3_deg 11.809 r_dihedral_angle_1_deg 9.078 r_rigid_bond_restr 2.776 r_angle_refined_deg 1.842 r_angle_other_deg 1.535 r_chiral_restr 0.109 r_bond_refined_d 0.014 r_gen_planes_refined 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.195 r_dihedral_angle_4_deg 16.701 r_dihedral_angle_3_deg 11.809 r_dihedral_angle_1_deg 9.078 r_rigid_bond_restr 2.776 r_angle_refined_deg 1.842 r_angle_other_deg 1.535 r_chiral_restr 0.109 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4061 Nucleic Acid Atoms Solvent Atoms 479 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing