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Structure of the SA2/Scc1/CENP_U complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QNX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 0.03 M CaCl2,0.03 M MgCl2,
0.1 M MOPS-HEPES, pH7.5,
10% PEG8000,
20% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.99 58.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.321 α = 90 b = 132.615 β = 90 c = 148.001 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 PILATUS3 6M 2023-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9785 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.52 49.43 99.15 0.059 0.042 0.999 10.39 2 19789
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.52 3.65 93.27 0.74 0.52 0.528 1.59 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MOLECULAR REPLACEMENT THROUGHOUT 3.52 49.43 18753 1036 99.16 0.22275 0.22017 0.2205 0.26943 0.2688 RANDOM 138.582
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] -2.43 1.27 1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.091 r_long_range_B_refined 24.074 r_long_range_B_other 24.074 r_dihedral_angle_3_deg 17.003 r_mcangle_it 16.782 r_mcangle_other 16.781 r_scangle_other 15.991 r_dihedral_angle_4_deg 14.706 r_mcbond_other 10.774 r_mcbond_it 10.773
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.091 r_long_range_B_refined 24.074 r_long_range_B_other 24.074 r_dihedral_angle_3_deg 17.003 r_mcangle_it 16.782 r_mcangle_other 16.781 r_scangle_other 15.991 r_dihedral_angle_4_deg 14.706 r_mcbond_other 10.774 r_mcbond_it 10.773 r_scbond_it 9.997 r_scbond_other 9.997 r_dihedral_angle_1_deg 5.546 r_angle_other_deg 1.607 r_angle_refined_deg 1.528 r_chiral_restr 0.095 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8141 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing