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PanDDA analysis group deposition -- Crystal Structure of human Brachyury in complex with Z1509882419
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 4.5 298 0.1 M CdCl, 0.1 M Acetate pH 4.5, 32% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.54 51.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.141 α = 90 b = 60.141 β = 90 c = 109.994 γ = 90
Symmetry Space Group P 41 2 2
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 2018-07-22 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 1.74 55.01 100 0.124 0.129 0.037 0.993 10.3 12.6 21501
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 1.74 1.79 100 2.283 2.375 0.651 0.799 13.1 1542
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 6f58 1.74 52.82 20415 1037 99.92 0.2254 0.2237 0.2619 0.3055 RANDOM 39.162
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] 1.64 1.64 -3.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.002 r_dihedral_angle_4_deg 20.278 r_dihedral_angle_3_deg 18.452 r_dihedral_angle_1_deg 8.053 r_mcangle_it 5.029 r_mcbond_other 3.065 r_mcbond_it 3.057 r_angle_refined_deg 1.532 r_angle_other_deg 1.279 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.002 r_dihedral_angle_4_deg 20.278 r_dihedral_angle_3_deg 18.452 r_dihedral_angle_1_deg 8.053 r_mcangle_it 5.029 r_mcbond_other 3.065 r_mcbond_it 3.057 r_angle_refined_deg 1.532 r_angle_other_deg 1.279 r_chiral_restr 0.073 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1369 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing