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PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z1272480091
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 2.9 57.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.984 α = 90 b = 167.688 β = 90 c = 47.106 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 2.66 113.82 100 0.13 0.154 0.061 0.997 7 6.3 36436
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 2.66 2.73 100 100 0.86 0.1073 0.433 0.365 1.3 6.1
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 2.66 113.82 34533 1832 99.79 0.2211 0.2175 0.2233 0.2879 0.2889 RANDOM 75.092
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] -5.66 0.67 4.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.673 r_dihedral_angle_3_deg 18.509 r_dihedral_angle_4_deg 15.994 r_mcangle_it 9.114 r_dihedral_angle_1_deg 6.946 r_mcbond_it 5.921 r_mcbond_other 5.918 r_angle_refined_deg 1.453 r_angle_other_deg 1.234 r_chiral_restr 0.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.673 r_dihedral_angle_3_deg 18.509 r_dihedral_angle_4_deg 15.994 r_mcangle_it 9.114 r_dihedral_angle_1_deg 6.946 r_mcbond_it 5.921 r_mcbond_other 5.918 r_angle_refined_deg 1.453 r_angle_other_deg 1.234 r_chiral_restr 0.067 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6922 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing