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Crystal structure of the Kelch domain of human KLHL12 with compound 10q
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 1.89 34.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.571 α = 90 b = 79.571 β = 90 c = 76.631 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 PIXEL DECTRIS EIGER2 S 9M 2023-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 0.98 ALS 8.2.1
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 1.271 56.329 96.4 0.051 1 25.2 10.7 59437
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 1.271 1.38 50.4 1.06 0.404 0.7 1.7
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 THROUGHOUT 1.271 56.329 59437 2836 91.234 0.162 0.1604 0.1894 0.1994 0.2155 12.324
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] 1.261 1.261 -2.523
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.917 r_dihedral_angle_3_deg 11.551 r_lrange_it 10.9 r_lrange_other 9.54 r_dihedral_angle_2_deg 8.815 r_dihedral_angle_1_deg 7.838 r_scangle_it 5.694 r_scangle_other 5.692 r_mcangle_other 4.581 r_mcangle_it 4.579
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.917 r_dihedral_angle_3_deg 11.551 r_lrange_it 10.9 r_lrange_other 9.54 r_dihedral_angle_2_deg 8.815 r_dihedral_angle_1_deg 7.838 r_scangle_it 5.694 r_scangle_other 5.692 r_mcangle_other 4.581 r_mcangle_it 4.579 r_scbond_it 3.833 r_scbond_other 3.823 r_rigid_bond_restr 3.523 r_mcbond_it 2.954 r_mcbond_other 2.951 r_angle_refined_deg 1.7 r_angle_other_deg 0.641 r_symmetry_nbd_refined 0.274 r_symmetry_xyhbond_nbd_other 0.267 r_nbd_other 0.23 r_symmetry_xyhbond_nbd_refined 0.22 r_xyhbond_nbd_refined 0.214 r_symmetry_nbd_other 0.204 r_nbd_refined 0.202 r_nbtor_refined 0.181 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2166 Nucleic Acid Atoms Solvent Atoms 274 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing