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PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z2447286438
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 61.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.598 α = 94.81 b = 72.046 β = 98.61 c = 118.412 γ = 115.22
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 2018-04-23 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 2.58 60.55 98 0.064 0.091 0.064 0.991 5.8 1.8 59775
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 2.58 2.65 97.3 0.504 0.713 0.504 0.492 1.7 4403
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 2.58 60.65 56804 2970 97.81 0.2323 0.2302 0.2336 0.2713 0.2724 RANDOM 85.573
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] 0.77 2.29 2.11 1.38 1.69 -6.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.969 r_dihedral_angle_4_deg 21.028 r_dihedral_angle_3_deg 20.226 r_dihedral_angle_1_deg 6.089 r_mcangle_it 3.721 r_mcbond_it 2.168 r_mcbond_other 2.168 r_angle_refined_deg 1.214 r_angle_other_deg 1.103 r_chiral_restr 0.048
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.969 r_dihedral_angle_4_deg 21.028 r_dihedral_angle_3_deg 20.226 r_dihedral_angle_1_deg 6.089 r_mcangle_it 3.721 r_mcbond_it 2.168 r_mcbond_other 2.168 r_angle_refined_deg 1.214 r_angle_other_deg 1.103 r_chiral_restr 0.048 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10033 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing