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Crystal structure of the Kelch domain of human KLHL12 with compound 10j
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 36.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.04 α = 90 b = 80.04 β = 90 c = 77.203 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 EIGER X 9M 2023-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.97933 NSLS-II 17-ID-1
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 1.01 56.6 92.8 0.01 0.015 0.01 1 37.6 1.9 120772
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 1.01 1.03 42.9 0.306 0.432 0.306 0.758 1.3
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 1.01 56.6 114666 6106 92.74 0.12603 0.12524 0.1338 0.14108 0.1468 RANDOM 12.095
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] 0.14 0.14 -0.28
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 12.911 r_dihedral_angle_3_deg 11.213 r_long_range_B_other 11.189 r_dihedral_angle_1_deg 7.823 r_scangle_other 7.519 r_dihedral_angle_2_deg 7.495 r_scbond_it 5.307 r_scbond_other 5.304 r_mcangle_other 5.264 r_mcangle_it 5.26
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 12.911 r_dihedral_angle_3_deg 11.213 r_long_range_B_other 11.189 r_dihedral_angle_1_deg 7.823 r_scangle_other 7.519 r_dihedral_angle_2_deg 7.495 r_scbond_it 5.307 r_scbond_other 5.304 r_mcangle_other 5.264 r_mcangle_it 5.26 r_rigid_bond_restr 4.293 r_mcbond_it 3.622 r_mcbond_other 3.607 r_angle_refined_deg 2.025 r_angle_other_deg 0.742 r_chiral_restr 0.119 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2195 Nucleic Acid Atoms Solvent Atoms 384 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction MOSFLM data reduction MOLREP phasing