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Crystal structure of the Kelch domain of human KLHL12 with compound 8i
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 1.9 35.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.891 α = 90 b = 79.891 β = 90 c = 76.67 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 2021-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.98 APS 21-ID-D
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 1.33 55.32 91.4 0.071 0.998 22.8 12.8 52105
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 1.33 1.36 100 0.193 0.988 11.4 12.9
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.334 45.521 52035 2657 91.378 0.164 0.1635 0.1785 0.1893 11.974
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] 0.126 0.126 -0.253
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.273 r_dihedral_angle_2_deg 11.546 r_dihedral_angle_3_deg 11.292 r_dihedral_angle_1_deg 7.961 r_lrange_it 5.057 r_scangle_it 3.176 r_scbond_it 2.104 r_mcangle_it 2.098 r_angle_refined_deg 2.07 r_mcbond_it 1.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.273 r_dihedral_angle_2_deg 11.546 r_dihedral_angle_3_deg 11.292 r_dihedral_angle_1_deg 7.961 r_lrange_it 5.057 r_scangle_it 3.176 r_scbond_it 2.104 r_mcangle_it 2.098 r_angle_refined_deg 2.07 r_mcbond_it 1.297 r_nbtor_refined 0.304 r_symmetry_xyhbond_nbd_refined 0.282 r_symmetry_nbd_refined 0.224 r_nbd_refined 0.204 r_xyhbond_nbd_refined 0.191 r_chiral_restr 0.127 r_gen_planes_refined 0.013 r_bond_refined_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2163 Nucleic Acid Atoms Solvent Atoms 364 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing