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The Crystal Structure of TGF beta R2 kinase domain from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5E8V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M Li2SO4, 0.1M Tris-HCl pH8.5, 30% PEG4,000
Crystal Properties Matthews coefficient Solvent content 2.5 50.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.09 α = 90 b = 75.02 β = 90 c = 77.704 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 PILATUS3 6M 2021-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1.18064 CLSI 08B1-1
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 2.1 48.03 100 0.999 19.4 6.4 21483
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 2.1 2.16 0.752
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.1 48.03 21432 1025 99.944 0.198 0.1949 0.2023 0.254 0.2556 44.21
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] 1.145 0.344 -1.488
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.482 r_dihedral_angle_3_deg 14.735 r_dihedral_angle_4_deg 12.892 r_lrange_it 7.679 r_lrange_other 7.667 r_dihedral_angle_1_deg 7.254 r_scangle_it 5.943 r_scangle_other 5.942 r_mcangle_it 4.982 r_mcangle_other 4.981
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.482 r_dihedral_angle_3_deg 14.735 r_dihedral_angle_4_deg 12.892 r_lrange_it 7.679 r_lrange_other 7.667 r_dihedral_angle_1_deg 7.254 r_scangle_it 5.943 r_scangle_other 5.942 r_mcangle_it 4.982 r_mcangle_other 4.981 r_scbond_it 3.998 r_scbond_other 3.997 r_mcbond_it 3.528 r_mcbond_other 3.522 r_angle_refined_deg 1.443 r_angle_other_deg 1.263 r_nbd_refined 0.204 r_xyhbond_nbd_refined 0.193 r_symmetry_nbd_other 0.179 r_symmetry_xyhbond_nbd_refined 0.171 r_nbd_other 0.167 r_nbtor_refined 0.165 r_symmetry_nbd_refined 0.152 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2310 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing