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Human transforming growth factor b type I receptor in complex with kinase inhibitor SB505124
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WOT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.6 291 23%(w/v) PEG 3350, 3%(v/v) glycerol
at pH 5.6
Crystal Properties Matthews coefficient Solvent content 2.13 42.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.07 α = 90 b = 79.846 β = 90 c = 87.8 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 DECTRIS EIGER2 R 1M 2022-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.87 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.9 59.07 100 0.997 8.2 15 12847
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.68 2.74 99.2 0.36
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 MOLECULAR REPLACEMENT THROUGHOUT 2.68 10.87 8038 404 96.24 0.21399 0.21223 0.2176 0.2477 0.2577 RANDOM 40.776
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] -0.09 0.87 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.41 r_dihedral_angle_3_deg 14.477 r_dihedral_angle_1_deg 10.844 r_long_range_B_refined 4.686 r_long_range_B_other 4.621 r_angle_refined_deg 2.241 r_mcangle_it 1.23 r_mcangle_other 1.23 r_angle_other_deg 1.195 r_scangle_other 1.142
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.41 r_dihedral_angle_3_deg 14.477 r_dihedral_angle_1_deg 10.844 r_long_range_B_refined 4.686 r_long_range_B_other 4.621 r_angle_refined_deg 2.241 r_mcangle_it 1.23 r_mcangle_other 1.23 r_angle_other_deg 1.195 r_scangle_other 1.142 r_mcbond_it 0.674 r_mcbond_other 0.674 r_scbond_it 0.648 r_scbond_other 0.648 r_chiral_restr 0.116 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.005 r_gen_planes_other 0.005 r_dihedral_angle_4_deg 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 2425 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement xia2 data reduction STARANISO data scaling REFMAC phasing