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TRK-A IN COMPLEX WITH LIGAND 1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277.15 The protein at a concentration of 10 mg/ml was mixed with 2mM of the ligand (diluted from 100 mM DMSO stock solution) for 1 hour on ice and crystallized at 4 deg C (hanging drop) from:
0.10 M KH2PO4/ 0.10 M NaH2PO4/ 0.10 M MES/NaOH pH 6.00 and 1.90 M NaCl (cryo: 25% glycerol in reservoir), or
18.00 % (w/v) PEG 3350, 0.20 M CaCl2, 0.10 M, MES pH=6.50 (cryo: direct).
Crystal Properties Matthews coefficient Solvent content 2.57 52.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.084 α = 90 b = 52.084 β = 90 c = 225.611 γ = 120
Symmetry Space Group P 31 1 2
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 EIGER X 16M 2015-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 2.19 75.2 99.1 0.038 21.78 4.1 18386
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 2.19 2.44 99.1 0.434 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.19 45.2 16947 1437 99.15 0.22743 0.22334 0.2276 0.27646 0.2798 RANDOM 52.878
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] 0.15 0.08 0.15 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.023 r_long_range_B_other 14.221 r_long_range_B_refined 14.189 r_dihedral_angle_3_deg 12.517 r_scangle_other 12.422 r_dihedral_angle_4_deg 11.034 r_mcangle_it 10.443 r_mcangle_other 10.442 r_scbond_it 9.583 r_scbond_other 9.579
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.023 r_long_range_B_other 14.221 r_long_range_B_refined 14.189 r_dihedral_angle_3_deg 12.517 r_scangle_other 12.422 r_dihedral_angle_4_deg 11.034 r_mcangle_it 10.443 r_mcangle_other 10.442 r_scbond_it 9.583 r_scbond_other 9.579 r_mcbond_it 8.282 r_mcbond_other 8.271 r_dihedral_angle_1_deg 5.28 r_angle_other_deg 2.544 r_angle_refined_deg 1.318 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 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 2319 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 30
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement Coot model building