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Crystal structure of human WD repeat-containing protein 5 in complex with 4-(3,5-dimethoxybenzyl)-9-(4-fluoro-2-methylphenyl)-7-((2-imino-3-methyl-2,3-dihydro-1H-imidazol-1-yl)methyl)-3,4-dihydrobenzo[f][1,4]oxazepin-5(2H)-one (compound 8)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EG6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 0.1 M Bis-Tris pH 7.0, 0.2 M ammonium acetate, 25% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.21 44.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.81 α = 88.04 b = 47.68 β = 89.27 c = 68.869 γ = 74.66
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-300 2018-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 2.01 28.658 90.4 0.079 0.112 0.079 0.996 7 3.9 34546
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 2.01 2.06 95.7 0.321 0.46 0.321 0.885 2.6 3.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.01 28.658 34545 1714 90.387 0.191 0.1884 0.1902 0.2322 0.2358 22.378
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] -0.913 -0.302 0.306 2.28 -0.024 -1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.079 r_dihedral_angle_other_2_deg 16.927 r_dihedral_angle_6_deg 14.223 r_dihedral_angle_3_deg 12.805 r_dihedral_angle_1_deg 8.222 r_lrange_it 7.028 r_lrange_other 6.845 r_scangle_it 3.872 r_scangle_other 3.871 r_mcangle_it 3.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.079 r_dihedral_angle_other_2_deg 16.927 r_dihedral_angle_6_deg 14.223 r_dihedral_angle_3_deg 12.805 r_dihedral_angle_1_deg 8.222 r_lrange_it 7.028 r_lrange_other 6.845 r_scangle_it 3.872 r_scangle_other 3.871 r_mcangle_it 3.79 r_mcangle_other 3.79 r_scbond_it 2.51 r_scbond_other 2.51 r_mcbond_it 2.473 r_mcbond_other 2.473 r_angle_refined_deg 1.532 r_angle_other_deg 0.526 r_symmetry_xyhbond_nbd_refined 0.25 r_xyhbond_nbd_refined 0.237 r_symmetry_nbd_refined 0.232 r_nbd_other 0.212 r_symmetry_nbd_other 0.202 r_nbd_refined 0.19 r_nbtor_refined 0.177 r_ncsr_local_group_1 0.089 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.073 r_symmetry_xyhbond_nbd_other 0.057 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4658 Nucleic Acid Atoms Solvent Atoms 480 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling MOLREP phasing