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Crystal structure of the Kelch domain of human KLHL12 with compound 10b
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 1.92 36.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.23 α = 90 b = 80.23 β = 90 c = 76.9 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 2022-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.99 APS 21-ID-D
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 1.4 56.73 99.9 0.162 0.169 0.045 0.997 10.7 13.6 50194
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 1.4 1.42 98.4 1.978 2.08 0.623 0.367 10.4
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 1.4 56.73 47522 2594 99.89 0.18083 0.17929 0.1877 0.20841 0.2149 RANDOM 15.048
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] -1.04 -1.04 2.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.889 r_dihedral_angle_3_deg 10.722 r_dihedral_angle_1_deg 8.015 r_long_range_B_refined 3.828 r_long_range_B_other 3.464 r_angle_refined_deg 1.756 r_scangle_other 1.708 r_mcangle_other 1.092 r_mcangle_it 1.089 r_scbond_it 1.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.889 r_dihedral_angle_3_deg 10.722 r_dihedral_angle_1_deg 8.015 r_long_range_B_refined 3.828 r_long_range_B_other 3.464 r_angle_refined_deg 1.756 r_scangle_other 1.708 r_mcangle_other 1.092 r_mcangle_it 1.089 r_scbond_it 1.072 r_scbond_other 1.072 r_angle_other_deg 0.628 r_mcbond_it 0.622 r_mcbond_other 0.621 r_chiral_restr 0.092 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 2189 Nucleic Acid Atoms Solvent Atoms 305 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction MOSFLM data reduction MOLREP phasing