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Crystal structure of the Kelch domain of human KLHL12 with compound 9c
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 35.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.67 α = 90 b = 79.67 β = 90 c = 77.26 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 2021-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 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 1.286 55.53 91.4 0.09 0.999 10.2 12.8 63553
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 1.286 1.31 100 0.471 0.98 4.2 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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.286 55.525 63553 3122 99.958 0.156 0.1547 0.1548 0.1772 0.1771 13.755
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] 0.189 0.189 -0.377
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.728 r_dihedral_angle_6_deg 16.266 r_dihedral_angle_3_deg 10.324 r_dihedral_angle_1_deg 8.089 r_lrange_it 4.215 r_lrange_other 3.893 r_scangle_it 2.834 r_scangle_other 2.833 r_angle_refined_deg 1.871 r_scbond_it 1.851
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.728 r_dihedral_angle_6_deg 16.266 r_dihedral_angle_3_deg 10.324 r_dihedral_angle_1_deg 8.089 r_lrange_it 4.215 r_lrange_other 3.893 r_scangle_it 2.834 r_scangle_other 2.833 r_angle_refined_deg 1.871 r_scbond_it 1.851 r_scbond_other 1.851 r_dihedral_angle_other_2_deg 1.572 r_mcangle_it 1.564 r_mcangle_other 1.563 r_mcbond_it 0.983 r_mcbond_other 0.978 r_angle_other_deg 0.671 r_symmetry_xyhbond_nbd_refined 0.289 r_nbd_refined 0.216 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.162 r_nbd_other 0.158 r_symmetry_xyhbond_nbd_other 0.103 r_chiral_restr 0.1 r_symmetry_nbd_refined 0.097 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 2186 Nucleic Acid Atoms Solvent Atoms 348 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing