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Structural basis for inhibition of human autotaxin by four novel compounds
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NKO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 20% PEG 3350, 0.4 M NaSCN
Crystal Properties Matthews coefficient Solvent content 2.42 49.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.616 α = 104.65 b = 70.488 β = 99.27 c = 107.374 γ = 99.86
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 RAYONIX MX-225 2013-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 1.00 APS 21-ID-G
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 1.8 50 96.2 0.057 7.3 2 154081
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 1.8 1.86 96 0.664 2 15375
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 3NKO 1.8 34.69 146325 7754 96.01 0.22259 0.22039 0.2274 0.265 0.2718 RANDOM 37.642
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.063 r_dihedral_angle_4_deg 16.428 r_dihedral_angle_3_deg 14.581 r_dihedral_angle_1_deg 6.436 r_long_range_B_refined 5.7 r_long_range_B_other 5.7 r_scangle_other 3.93 r_mcangle_it 3.393 r_mcangle_other 3.393 r_scbond_it 2.627
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.063 r_dihedral_angle_4_deg 16.428 r_dihedral_angle_3_deg 14.581 r_dihedral_angle_1_deg 6.436 r_long_range_B_refined 5.7 r_long_range_B_other 5.7 r_scangle_other 3.93 r_mcangle_it 3.393 r_mcangle_other 3.393 r_scbond_it 2.627 r_scbond_other 2.621 r_mcbond_it 2.384 r_mcbond_other 2.381 r_angle_refined_deg 1.508 r_angle_other_deg 0.834 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 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 11957 Nucleic Acid Atoms Solvent Atoms 614 Heterogen Atoms 198
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing PDB_EXTRACT data extraction