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Crystal structure of murine autotaxin in complex with a small molecule inhibitor
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 20-25% PEG3350, 0.5M KSCN, 0.2mM ZnSO4, 1% (w/v) polyvinylpyrrolidone K15
Crystal Properties Matthews coefficient Solvent content 2.42 49.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.16 α = 85.77 b = 61.58 β = 72.68 c = 66.14 γ = 80.21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2012-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.92 60.66 97.2 0.065 11.1 3.9 67396
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 1.92 1.97 96 0.595 2.2 3.9
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 3NKM 1.92 50 63984 3410 97.23 0.16191 0.1598 0.1685 0.20115 0.205 RANDOM 35.324
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] -0.61 -0.7 0.85 -0.62 -0.55 1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.997 r_dihedral_angle_4_deg 17.439 r_dihedral_angle_3_deg 14.366 r_dihedral_angle_1_deg 10.325 r_long_range_B_refined 6.231 r_long_range_B_other 6.231 r_scangle_other 3.353 r_mcangle_it 2.416 r_mcangle_other 2.416 r_scbond_it 2.211
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.997 r_dihedral_angle_4_deg 17.439 r_dihedral_angle_3_deg 14.366 r_dihedral_angle_1_deg 10.325 r_long_range_B_refined 6.231 r_long_range_B_other 6.231 r_scangle_other 3.353 r_mcangle_it 2.416 r_mcangle_other 2.416 r_scbond_it 2.211 r_scbond_other 2.211 r_angle_refined_deg 1.92 r_mcbond_it 1.596 r_mcbond_other 1.594 r_angle_other_deg 0.951 r_chiral_restr 0.121 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6333 Nucleic Acid Atoms Solvent Atoms 427 Heterogen Atoms 143
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing