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Crystal Structure of rat Autotaxin in complex with 3-[4-(cyclopropylmethoxy)naphthalen-2-yl]-4-methyl-1H-1,2,4-triazol-5-one
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model in house model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293 15.3 mg/mL protein in 20mM BICINE/NaOH pH8.5, 150mM NaCl, 0.02% NaN3 mixed 50-70% with 50-30% reservoir consisting of 11-17% PEG3350, 0.1M Na-acetate pH4.5, 0.2M Ca-acetate, total volume 200nL
Crystal Properties Matthews coefficient Solvent content 2.34 47.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.858 α = 90 b = 91.338 β = 90 c = 118.705 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 PSI PILATUS 6M 2013-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000010 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.94 48.45 99.9 0.111 0.121 0.998 13.56 6.642 68150 35.153
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 1.99 100 1.088 1.179 0.658 1.97 6.737
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 inhouse model 1.94 48.45 62741 3349 97 0.1841 0.1823 0.2179 0.1984 RANDOM 32.928
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] -0.17 -0.23 0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.678 r_dihedral_angle_4_deg 15.927 r_dihedral_angle_3_deg 13.147 r_dihedral_angle_1_deg 6.12 r_angle_refined_deg 1.416 r_chiral_restr 0.1 r_bond_refined_d 0.011 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6508 Nucleic Acid Atoms Solvent Atoms 421 Heterogen Atoms 121
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing