☰ Navigation Tabs
PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z2856434884
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 3.16 61.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.489 α = 94.89 b = 72.409 β = 98.6 c = 118.515 γ = 115.59
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 2018-09-20 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 3.03 115.5 98.3 0.072 0.101 0.072 0.994 6.4 1.8 37042
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 3.03 3.11 98.1 0.635 0.898 0.635 0.61 1.8 2747
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 3.03 115.52 35191 1844 98.08 0.1914 0.1873 0.2014 0.2672 0.2694 RANDOM 90.959
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] 2.94 2.17 3.56 -0.42 1.09 -5.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.017 r_dihedral_angle_4_deg 21.396 r_dihedral_angle_3_deg 21.116 r_mcangle_it 11.114 r_mcbond_it 7.5 r_mcbond_other 7.499 r_dihedral_angle_1_deg 7.112 r_angle_refined_deg 1.521 r_angle_other_deg 1.276 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.017 r_dihedral_angle_4_deg 21.396 r_dihedral_angle_3_deg 21.116 r_mcangle_it 11.114 r_mcbond_it 7.5 r_mcbond_other 7.499 r_dihedral_angle_1_deg 7.112 r_angle_refined_deg 1.521 r_angle_other_deg 1.276 r_chiral_restr 0.07 r_bond_refined_d 0.007 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 157 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing