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PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z2856434783
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QB5 6qb5
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 3.14 60.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.443 α = 95.13 b = 71.748 β = 99.21 c = 118.782 γ = 115.27
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 2018-07-02 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 2.76 60.64 95.3 0.041 0.058 0.041 0.999 10.1 1.8 47491
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 2.76 2.9 96.8 0.858 1.213 0.858 0.465 1.9 7032
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 6qb5 2.76 58.68 45816 2393 97.3 0.2009 0.1975 0.2083 0.2639 0.2631 RANDOM 95.044
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] 0.93 1.45 4.14 -0.65 1.55 -3.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.679 r_dihedral_angle_4_deg 21.483 r_dihedral_angle_3_deg 21.204 r_mcangle_it 11.158 r_mcbond_other 7.762 r_mcbond_it 7.761 r_dihedral_angle_1_deg 7.102 r_angle_refined_deg 1.506 r_angle_other_deg 1.264 r_chiral_restr 0.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.679 r_dihedral_angle_4_deg 21.483 r_dihedral_angle_3_deg 21.204 r_mcangle_it 11.158 r_mcbond_other 7.762 r_mcbond_it 7.761 r_dihedral_angle_1_deg 7.102 r_angle_refined_deg 1.506 r_angle_other_deg 1.264 r_chiral_restr 0.069 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10037 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing