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Crystal structure of the Kelch domain of human KLHL12 with compound 8m
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 1.83 32.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.633 α = 90 b = 79.633 β = 90 c = 74.382 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 2022-03-02 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) 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 1.308 33.72 99.2 0.132 0.997 8.4 11.4 45864
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 1.308 1.33 78.6 0.561 0.382 1 10.7
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 FREE R-VALUE 1.308 33.72 45864 2280 78.749 0.161 0.1586 0.1671 0.2038 0.203 14.441
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] 0.497 0.497 -0.993
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.293 r_dihedral_angle_3_deg 12.09 r_dihedral_angle_2_deg 10.66 r_lrange_it 9.802 r_lrange_other 8.007 r_dihedral_angle_1_deg 7.721 r_scangle_it 5.152 r_scangle_other 5.15 r_rigid_bond_restr 3.925 r_mcangle_other 3.901
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.293 r_dihedral_angle_3_deg 12.09 r_dihedral_angle_2_deg 10.66 r_lrange_it 9.802 r_lrange_other 8.007 r_dihedral_angle_1_deg 7.721 r_scangle_it 5.152 r_scangle_other 5.15 r_rigid_bond_restr 3.925 r_mcangle_other 3.901 r_mcangle_it 3.895 r_scbond_it 3.577 r_scbond_other 3.576 r_mcbond_it 2.637 r_mcbond_other 2.611 r_angle_refined_deg 1.907 r_angle_other_deg 0.703 r_symmetry_xyhbond_nbd_refined 0.337 r_xyhbond_nbd_refined 0.269 r_symmetry_nbd_refined 0.234 r_nbd_other 0.228 r_nbd_refined 0.208 r_symmetry_nbd_other 0.189 r_symmetry_xyhbond_nbd_other 0.182 r_nbtor_refined 0.175 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 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 308 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing