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Crystal structure of autotaxin (ENPP2) re-refined
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GSN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 Protein buffer: 3.5-5.0 mg/ml autotaxin in 50 mM Tris pH 8.0 and 150 mM NaCl
Crystallization condition: 20% PEG 3350, 0.2 M ammonium iodide, 0.3 M sodium thiocyanate
Crystal Properties Matthews coefficient Solvent content 2.2 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.808 α = 98.78 b = 63.289 β = 106.22 c = 70.471 γ = 99.77
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.283 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.05 20 96.8 0.1 13.9 4.8 52153 30.2
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 2.05 2.12 93.9 0.38 2.49 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2GSN 2.05 20 45374 2386 88.53 0.1562 0.154 0.1647 0.1974 0.2037 RANDOM 42.438
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] 0.83 -0.24 0.85 -0.08 -0.27 -0.83
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 37.045 r_sphericity_free 33.959 r_dihedral_angle_2_deg 33.349 r_dihedral_angle_4_deg 15.746 r_dihedral_angle_3_deg 11.711 r_dihedral_angle_1_deg 6.171 r_mcangle_it 3.68 r_mcbond_it 2.562 r_mcbond_other 2.542 r_angle_refined_deg 1.36
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 37.045 r_sphericity_free 33.959 r_dihedral_angle_2_deg 33.349 r_dihedral_angle_4_deg 15.746 r_dihedral_angle_3_deg 11.711 r_dihedral_angle_1_deg 6.171 r_mcangle_it 3.68 r_mcbond_it 2.562 r_mcbond_other 2.542 r_angle_refined_deg 1.36 r_angle_other_deg 0.941 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6329 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 121
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Coot model building DENZO data reduction