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Crystal structure of Chi430 mutant E176A in the substrate complex
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 290 0.1 M BIS-TRIS pH 5.5, 2.0 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.48 50.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.676 α = 90 b = 49.858 β = 125.62 c = 92.602 γ = 90
Symmetry Space Group C 1 2 1
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 16M 2025-01-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.97918 SSRF BL10U2
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.35 60.58 99.8 0.974 7.4 6 98938 6.58
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.39 0.189 2.5 4.4
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 1.35 49.51 94012 4902 99.77 0.18514 0.1842 0.1936 0.20328 0.2112 RANDOM 10.787
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] -0.06 0.24 -0.41 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.533 r_dihedral_angle_1_deg 6.28 r_long_range_B_refined 4.679 r_long_range_B_other 4.664 r_dihedral_angle_2_deg 4.058 r_scangle_other 3.814 r_scbond_other 2.438 r_scbond_it 2.436 r_mcangle_it 1.97 r_mcangle_other 1.969
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.533 r_dihedral_angle_1_deg 6.28 r_long_range_B_refined 4.679 r_long_range_B_other 4.664 r_dihedral_angle_2_deg 4.058 r_scangle_other 3.814 r_scbond_other 2.438 r_scbond_it 2.436 r_mcangle_it 1.97 r_mcangle_other 1.969 r_angle_refined_deg 1.959 r_mcbond_it 1.269 r_mcbond_other 1.269 r_angle_other_deg 0.69 r_chiral_restr 0.104 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 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 3295 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHENIX phasing