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PanDDA analysis group deposition -- Crystal Structure of human Brachyury G177D variant in complex with Z2856434868
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 48.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.38 α = 90 b = 99.38 β = 90 c = 99.29 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 1.85 42.99 100 0.113 0.119 0.038 0.999 11.8 9.7 16263
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 1.85 1.9 100 1.654 1.743 0.546 0.628 10.1 1191
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 1.9 49.69 14119 741 98.87 0.194 0.1908 0.2164 0.2534 0.2689 RANDOM 34.94
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.511 r_dihedral_angle_4_deg 21.463 r_dihedral_angle_3_deg 15.803 r_dihedral_angle_1_deg 6.996 r_mcangle_it 3.582 r_mcbond_other 2.328 r_mcbond_it 2.323 r_angle_refined_deg 1.468 r_angle_other_deg 1.28 r_chiral_restr 0.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.511 r_dihedral_angle_4_deg 21.463 r_dihedral_angle_3_deg 15.803 r_dihedral_angle_1_deg 6.996 r_mcangle_it 3.582 r_mcbond_other 2.328 r_mcbond_it 2.323 r_angle_refined_deg 1.468 r_angle_other_deg 1.28 r_chiral_restr 0.062 r_bond_refined_d 0.014 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 1380 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing