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PanDDA analysis group deposition -- Crystal Structure of human Brachyury G177D variant in complex with Z1432018343
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 2.43 49.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.934 α = 90 b = 99.934 β = 90 c = 99.314 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 2018-12-08 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 1.47 49.98 100 0.041 0.044 0.014 1 19.9 8.4 32536
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 1.47 1.51 100 1.306 1.441 0.599 0.593 5.7 2375
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 1.47 49.97 30948 1578 99.96 0.2125 0.2114 0.2238 0.2342 0.2538 RANDOM 24.549
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] -0.51 -0.26 -0.51 1.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.319 r_dihedral_angle_3_deg 13.542 r_dihedral_angle_4_deg 10.77 r_dihedral_angle_1_deg 6.578 r_mcangle_it 2.095 r_angle_refined_deg 1.432 r_angle_other_deg 1.241 r_mcbond_it 1.219 r_mcbond_other 1.214 r_chiral_restr 0.053
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.319 r_dihedral_angle_3_deg 13.542 r_dihedral_angle_4_deg 10.77 r_dihedral_angle_1_deg 6.578 r_mcangle_it 2.095 r_angle_refined_deg 1.432 r_angle_other_deg 1.241 r_mcbond_it 1.219 r_mcbond_other 1.214 r_chiral_restr 0.053 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1380 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing