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Structure of Autotaxin (ENPP2) with LM350
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, SITTING DROP 293 22% PEG 3350, NH4I (0.2M), NaSCN (0.1M)
Crystal Properties Matthews coefficient Solvent content 2.22 44.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.655 α = 90 b = 89.067 β = 102.88 c = 77.509 γ = 90
Symmetry Space Group P 1 21 1
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 2016-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.97925 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 2.4 46 99.6 0.074 0.09 0.05 0.998 12.9 3 32432
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 99.4 0.655 0.784 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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2XR9 2.4 46 30843 1569 99.54 0.2194 0.2173 0.2621 0.2271 RANDOM 61.503
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] -2.2 0.69 2.5 -0.56
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 65.955 r_dihedral_angle_2_deg 33.238 r_dihedral_angle_4_deg 14.71 r_dihedral_angle_3_deg 13.051 r_dihedral_angle_1_deg 6.353 r_angle_refined_deg 1.207 r_angle_other_deg 0.951 r_mcangle_it 0.874 r_mcbond_it 0.471 r_mcbond_other 0.471
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 65.955 r_dihedral_angle_2_deg 33.238 r_dihedral_angle_4_deg 14.71 r_dihedral_angle_3_deg 13.051 r_dihedral_angle_1_deg 6.353 r_angle_refined_deg 1.207 r_angle_other_deg 0.951 r_mcangle_it 0.874 r_mcbond_it 0.471 r_mcbond_other 0.471 r_chiral_restr 0.092 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6252 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 135
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction