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DaCS-intermediate complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold A0A7C6A739
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289.15 0.1M HEPES pH7.5, 40% v/v Polyethylene glycol 400
Crystal Properties Matthews coefficient Solvent content 2.5 50.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 361.422 α = 90 b = 361.422 β = 90 c = 77.741 γ = 120
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 EIGER X 4M 2021-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.979 SSRF BL18U1
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 2.029 50 99.1 0.185 0.199 0.072 0.989 14.5 7.3 242593
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.029 2.07 0.983 0.68
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 2.03 25.07 223879 11849 96.2 0.198 0.196 0.2041 0.239 0.2456 RANDOM 33.22
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] -0.04 -0.02 -0.04 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.907 r_long_range_B_refined 9.892 r_dihedral_angle_2_deg 9.817 r_long_range_B_other 9.724 r_dihedral_angle_1_deg 6.88 r_scangle_other 4.453 r_mcangle_it 4.156 r_mcangle_other 4.156 r_scbond_it 2.852 r_scbond_other 2.852
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.907 r_long_range_B_refined 9.892 r_dihedral_angle_2_deg 9.817 r_long_range_B_other 9.724 r_dihedral_angle_1_deg 6.88 r_scangle_other 4.453 r_mcangle_it 4.156 r_mcangle_other 4.156 r_scbond_it 2.852 r_scbond_other 2.852 r_mcbond_it 2.775 r_mcbond_other 2.775 r_angle_refined_deg 1.428 r_angle_other_deg 0.48 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 27401 Nucleic Acid Atoms Solvent Atoms 2026 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing