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Crystal structure of Autotaxin (ENPP2) with 18F-labeled positron emission tomography ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XR9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 PEG3350, NaSCN, NH4I
Crystal Properties Matthews coefficient Solvent content 2.2 44.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.57 α = 90 b = 87.149 β = 90 c = 145.361 γ = 90
Symmetry Space Group P 21 21 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 2M-F 2019-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.999998 SLS X06DA
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 2.2 48.45 98.4 0.193 0.234 0.13 0.977 4.6 5.4 39684
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 2.2 2.27 1.029 1.248 0.694 0.656 5.3
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2xr9 2.2 47.568 39641 1926 97.913 0.215 0.2124 0.2708 0.2887 34.843
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] -0.97 2.433 -1.463
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.573 r_dihedral_angle_4_deg 14.723 r_dihedral_angle_3_deg 12.777 r_dihedral_angle_1_deg 7.09 r_lrange_it 5.065 r_lrange_other 5.041 r_scangle_it 3.288 r_scangle_other 3.288 r_mcangle_other 2.821 r_mcangle_it 2.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.573 r_dihedral_angle_4_deg 14.723 r_dihedral_angle_3_deg 12.777 r_dihedral_angle_1_deg 7.09 r_lrange_it 5.065 r_lrange_other 5.041 r_scangle_it 3.288 r_scangle_other 3.288 r_mcangle_other 2.821 r_mcangle_it 2.82 r_scbond_it 2.187 r_scbond_other 2.186 r_mcbond_it 1.853 r_mcbond_other 1.832 r_angle_refined_deg 1.337 r_angle_other_deg 1.148 r_nbd_other 0.191 r_nbd_refined 0.187 r_symmetry_nbd_other 0.177 r_symmetry_nbd_refined 0.172 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.158 r_symmetry_xyhbond_nbd_refined 0.146 r_metal_ion_refined 0.131 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.052 r_symmetry_xyhbond_nbd_other 0.023 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6221 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms 153
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Coot model building XDS data reduction Aimless data scaling MOLREP phasing