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Crystal structure of autotaxin with orthovanadate bound as a trigonal bipyramidal intermediate analog
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DLT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 Protein buffer: 4.5 mg/ml autotaxin, incubated with 1 mM orthovanadate, 20 mM hepes pH 7.4, 150 mM NaCl
Crystallisation condition: 18% (w/v) PEG3350, 0.2 M NH4I, 0.4M NaSCN
Crystal Properties Matthews coefficient Solvent content 2.34 47.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.75 α = 99.33 b = 63.45 β = 105.91 c = 70.55 γ = 99.51
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 2010-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.9792 SLS X06DA
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 2.2 40 90.2 0.116 4.9 1.6 39503
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 2.2 2.32 90.7 0.825 1.4 1.7
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 5dlt 2.2 40 37463 2000 90.06 0.2043 0.2025 0.2086 0.2391 0.2388 RANDOM 42.948
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] -0.27 1.84 -0.24 -0.47 0.89 -0.15
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 45.775 r_dihedral_angle_2_deg 34.909 r_dihedral_angle_4_deg 15.983 r_dihedral_angle_3_deg 11.971 r_dihedral_angle_1_deg 6.06 r_mcangle_it 3.143 r_mcbond_it 1.962 r_mcbond_other 1.957 r_angle_refined_deg 1.231 r_angle_other_deg 0.894
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 45.775 r_dihedral_angle_2_deg 34.909 r_dihedral_angle_4_deg 15.983 r_dihedral_angle_3_deg 11.971 r_dihedral_angle_1_deg 6.06 r_mcangle_it 3.143 r_mcbond_it 1.962 r_mcbond_other 1.957 r_angle_refined_deg 1.231 r_angle_other_deg 0.894 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6337 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 68
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Coot model building PDB-REDO refinement