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Crystal structure of de novo designed binder JUBO4 and the LEDGF PWWP domain
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 293 1.4 M Trisodium citrate
0.1 M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.84 67.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.297 α = 90 b = 79.297 β = 90 c = 77.954 γ = 120
Symmetry Space Group P 31 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 EIGER2 X 9M 2024-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87313 ESRF ID23-2
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 2.1 68.67 100 0.31 0.323 0.091 0.996 7.4 12.4 17093
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 2.1 2.21 100 4.202 4.379 1.227 0.613 12.5
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 2.1 68.67 16184 867 99.87 0.19557 0.19374 0.2018 0.23127 0.2407 RANDOM 41.68
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] 1.08 0.54 1.08 -3.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.421 r_long_range_B_refined 10.192 r_long_range_B_other 10.17 r_scangle_other 8.447 r_dihedral_angle_1_deg 7.37 r_dihedral_angle_2_deg 7.136 r_mcangle_it 5.658 r_mcangle_other 5.655 r_scbond_it 5.416 r_scbond_other 5.412
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.421 r_long_range_B_refined 10.192 r_long_range_B_other 10.17 r_scangle_other 8.447 r_dihedral_angle_1_deg 7.37 r_dihedral_angle_2_deg 7.136 r_mcangle_it 5.658 r_mcangle_other 5.655 r_scbond_it 5.416 r_scbond_other 5.412 r_mcbond_it 3.916 r_mcbond_other 3.915 r_angle_refined_deg 1.968 r_angle_other_deg 0.626 r_chiral_restr 0.08 r_bond_refined_d 0.008 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 1276 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing