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PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z1267773786
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6R7O 6r7o
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Crystal Properties Matthews coefficient Solvent content 2.93 58.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.972 α = 90 b = 167.338 β = 90 c = 47.677 γ = 90
Symmetry Space Group P 21 21 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 2018-04-13 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 3.08 83.68 100 0.211 0.23 0.091 0.993 5.6 6.4 23924
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 3.08 3.16 100 0.851 0.922 0.354 0.708 6.6 1777
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 6r7o 3.08 113.7 22672 1202 99.94 0.2314 0.2281 0.2375 0.2919 0.2997 RANDOM 81.623
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] -7.48 -1.73 9.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.969 r_dihedral_angle_3_deg 17.584 r_dihedral_angle_4_deg 16.181 r_mcangle_it 7.955 r_dihedral_angle_1_deg 6.623 r_mcbond_it 4.853 r_mcbond_other 4.836 r_angle_refined_deg 1.37 r_angle_other_deg 0.973 r_chiral_restr 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.969 r_dihedral_angle_3_deg 17.584 r_dihedral_angle_4_deg 16.181 r_mcangle_it 7.955 r_dihedral_angle_1_deg 6.623 r_mcbond_it 4.853 r_mcbond_other 4.836 r_angle_refined_deg 1.37 r_angle_other_deg 0.973 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6922 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing