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PanDDA analysis group deposition -- Crystal Structure of human Brachyury in complex with Z30820160
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 2.53 51.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.99 α = 90 b = 59.99 β = 90 c = 110.22 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 1.65 55.11 99.4 0.069 0.072 0.02 0.999 16.1 12.7 24822
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 1.65 1.69 98.7 2.315 2.421 0.698 0.606 11.8 1774
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 1.65 52.75 23597 1202 99.2 0.22 0.2186 0.2348 0.2493 0.253 RANDOM 42.063
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] 1.37 1.37 -2.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.078 r_dihedral_angle_3_deg 17.973 r_dihedral_angle_1_deg 7.78 r_dihedral_angle_4_deg 5.885 r_mcangle_it 5.816 r_mcbond_it 3.756 r_mcbond_other 3.751 r_angle_refined_deg 1.685 r_angle_other_deg 1.363 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.078 r_dihedral_angle_3_deg 17.973 r_dihedral_angle_1_deg 7.78 r_dihedral_angle_4_deg 5.885 r_mcangle_it 5.816 r_mcbond_it 3.756 r_mcbond_other 3.751 r_angle_refined_deg 1.685 r_angle_other_deg 1.363 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 71 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing