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Crystal Structure of Autotaxin in Complex with 4BoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NKM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 23% PEG3350, 0.15M NaCl, 0.5M KSCN, 0.2mM ZnSO4, 1% polyvinylpyrrolidone, vapor diffusion, sitting drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.28 46.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.556 α = 90 b = 94.524 β = 93.98 c = 75.242 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 CCD 2011-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.000 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.746 50 85267 21.54
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 3NKM 1.746 49.234 1.51 85244 4277 97.87 0.1829 0.1809 0.1782 0.2209 0.219 30.2064
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] -1.3274 -0.4089 3.3616 -2.0343
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.458 f_angle_d 1.657 f_chiral_restr 0.124 f_bond_d 0.018 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6307 Nucleic Acid Atoms Solvent Atoms 452 Heterogen Atoms 221
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing