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PanDDA analysis group deposition -- Crystal Structure of human Brachyury G177D variant in complex with Z321318226
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6F58 6f58
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 0.1 M SPG pH 7.0, 30 % PEG 1000
Crystal Properties Matthews coefficient Solvent content 2.4 48.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.93 α = 90 b = 99.93 β = 90 c = 98.02 γ = 120
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 PILATUS 6M 2018-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.02 42.54 100 0.135 0.143 0.047 0.991 9.5 9.4 12422
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.02 2.07 100 1.348 1.439 0.496 0.755 9.1 908
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 FOURIER SYNTHESIS THROUGHOUT 6f58 2.1 49.97 10506 521 98.69 0.1891 0.1858 0.2064 0.2568 0.272 RANDOM 46.229
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] -0.75 -0.37 -0.75 2.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.733 r_dihedral_angle_4_deg 18.899 r_dihedral_angle_3_deg 15.124 r_dihedral_angle_1_deg 6.718 r_mcangle_it 4.982 r_mcbond_other 3.368 r_mcbond_it 3.36 r_angle_refined_deg 1.586 r_angle_other_deg 1.25 r_chiral_restr 0.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.733 r_dihedral_angle_4_deg 18.899 r_dihedral_angle_3_deg 15.124 r_dihedral_angle_1_deg 6.718 r_mcangle_it 4.982 r_mcbond_other 3.368 r_mcbond_it 3.36 r_angle_refined_deg 1.586 r_angle_other_deg 1.25 r_chiral_restr 0.068 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1380 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing