☰ Navigation Tabs
Crystal structure of the Kelch domain of human KLHL12 with compound 9h
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 34.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.78 α = 90 b = 79.78 β = 90 c = 76.37 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 2021-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.98 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 1.33 55.23 100 0.086 0.997 18.3 13 56571
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 1.33 1.37 100 0.245 0.984 8.2 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 1.334 55.229 56571 2885 99.993 0.161 0.1599 0.1604 0.1727 0.1596 12.048
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] -0.149 -0.149 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.24 r_dihedral_angle_3_deg 10.985 r_dihedral_angle_2_deg 8.242 r_dihedral_angle_1_deg 8.052 r_lrange_it 4.096 r_lrange_other 3.618 r_scangle_it 2.295 r_scangle_other 2.294 r_angle_refined_deg 1.872 r_mcangle_it 1.736
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.24 r_dihedral_angle_3_deg 10.985 r_dihedral_angle_2_deg 8.242 r_dihedral_angle_1_deg 8.052 r_lrange_it 4.096 r_lrange_other 3.618 r_scangle_it 2.295 r_scangle_other 2.294 r_angle_refined_deg 1.872 r_mcangle_it 1.736 r_mcangle_other 1.736 r_scbond_it 1.489 r_scbond_other 1.489 r_mcbond_it 1.053 r_mcbond_other 1.043 r_angle_other_deg 0.671 r_symmetry_nbd_refined 0.236 r_xyhbond_nbd_refined 0.229 r_symmetry_xyhbond_nbd_other 0.225 r_nbd_refined 0.212 r_symmetry_nbd_other 0.197 r_symmetry_xyhbond_nbd_refined 0.194 r_nbtor_refined 0.179 r_nbd_other 0.171 r_chiral_restr 0.096 r_symmetry_nbtor_other 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2163 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing