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Crystal structure of the Kelch domain of human KLHL12 with compound 9k
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 35.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.79 α = 90 b = 79.79 β = 90 c = 76.89 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 2021-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.98004 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 56.484 100 0.067 0.994 19.7 12.6 63441
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 1.29 1.31 100 0.357 0.967 6.5 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 56.484 63441 3198 99.948 0.152 0.1507 0.151 0.1701 0.1702 13.078
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] -0.256 -0.256 0.511
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.53 r_dihedral_angle_6_deg 16.512 r_dihedral_angle_3_deg 10.08 r_dihedral_angle_1_deg 8.113 r_dihedral_angle_other_2_deg 5.244 r_lrange_it 4.253 r_lrange_other 3.784 r_scangle_it 2.793 r_scangle_other 2.792 r_angle_refined_deg 1.784
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.53 r_dihedral_angle_6_deg 16.512 r_dihedral_angle_3_deg 10.08 r_dihedral_angle_1_deg 8.113 r_dihedral_angle_other_2_deg 5.244 r_lrange_it 4.253 r_lrange_other 3.784 r_scangle_it 2.793 r_scangle_other 2.792 r_angle_refined_deg 1.784 r_scbond_it 1.784 r_scbond_other 1.782 r_mcangle_it 1.503 r_mcangle_other 1.503 r_mcbond_it 0.935 r_mcbond_other 0.935 r_angle_other_deg 0.64 r_nbd_refined 0.205 r_symmetry_xyhbond_nbd_refined 0.198 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.16 r_nbd_other 0.137 r_symmetry_nbd_refined 0.119 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.011 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 366 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing