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Crystal structure of the Kelch domain of human KLHL12 with compound 9e
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VPJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.1M Bis-Tris pH 5.5, 0.2M MgCl2 and 25% PEG3350
Crystal Properties Matthews coefficient Solvent content 1.91 35.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.95 α = 90 b = 79.95 β = 90 c = 76.8 γ = 90
Symmetry Space Group P 41 21 2
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 MARMOSAIC 300 mm CCD Beryllium Lenses 2021-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97872 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.2 35.78 100 0.071 0.999 19 14.1 78068
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 1.2 1.22 99.8 0.366 0.965 5.8 13.7
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 1.2 35.78 78068 4014 99.99 0.134 0.1326 0.1415 0.1521 0.1591 11.099
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] -0.482 -0.482 0.964
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.664 r_dihedral_angle_6_deg 16.769 r_dihedral_angle_3_deg 10.907 r_lrange_it 8.312 r_dihedral_angle_1_deg 8.244 r_lrange_other 6.769 r_rigid_bond_restr 4.586 r_scangle_it 4.04 r_scangle_other 4.04 r_mcangle_other 3.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.664 r_dihedral_angle_6_deg 16.769 r_dihedral_angle_3_deg 10.907 r_lrange_it 8.312 r_dihedral_angle_1_deg 8.244 r_lrange_other 6.769 r_rigid_bond_restr 4.586 r_scangle_it 4.04 r_scangle_other 4.04 r_mcangle_other 3.132 r_mcangle_it 3.128 r_scbond_other 2.813 r_scbond_it 2.812 r_dihedral_angle_other_2_deg 2.028 r_mcbond_it 1.987 r_mcbond_other 1.973 r_angle_refined_deg 1.94 r_angle_other_deg 0.728 r_symmetry_xyhbond_nbd_refined 0.317 r_nbd_refined 0.213 r_symmetry_nbd_refined 0.205 r_symmetry_nbd_other 0.19 r_xyhbond_nbd_refined 0.19 r_nbd_other 0.178 r_nbtor_refined 0.177 r_chiral_restr 0.114 r_symmetry_nbtor_other 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2163 Nucleic Acid Atoms Solvent Atoms 362 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing