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X-ray crystallographic structure of SwaQ2 in complex with NADP+ and doxorubicin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5L3Z ligand a solvent free coordinate file was used
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.67 277 0.1 M NaCacodylate pH6.67, 1M Na3-CITRATE
Crystal Properties Matthews coefficient Solvent content 3.05 59.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.313 α = 90 b = 87.313 β = 90 c = 174.382 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 110 PIXEL DECTRIS EIGER X 16M MIRRORS 2022-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.976254 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.4 29.08 94.2 0.173 0.087 0.992 6.9 4.1 27570 39.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 93.8 0.774 0.523 0.722 2 4.1
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 2.4 29.08 26051 1444 93.59 0.16353 0.16127 0.1738 0.20344 0.2149 RANDOM 41.083
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] 0.79 0.4 0.79 -2.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.08 r_dihedral_angle_4_deg 19.752 r_dihedral_angle_3_deg 14.529 r_dihedral_angle_1_deg 6.853 r_long_range_B_refined 6.342 r_long_range_B_other 6.287 r_scangle_other 3.033 r_mcangle_it 2.335 r_mcangle_other 2.335 r_angle_refined_deg 1.814
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.08 r_dihedral_angle_4_deg 19.752 r_dihedral_angle_3_deg 14.529 r_dihedral_angle_1_deg 6.853 r_long_range_B_refined 6.342 r_long_range_B_other 6.287 r_scangle_other 3.033 r_mcangle_it 2.335 r_mcangle_other 2.335 r_angle_refined_deg 1.814 r_scbond_it 1.789 r_scbond_other 1.789 r_angle_other_deg 1.382 r_mcbond_it 1.339 r_mcbond_other 1.338 r_chiral_restr 0.076 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 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 4182 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 252
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing