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Crystal structure of the kelch domain of human KLHL2 (Mayven)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ADE PDB ENTRY 3ADE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.2M (NH4)2SO4, 0.1M MES PH 6.5, 30% PEG 5000 MME, 0.2M NASCN
Crystal Properties Matthews coefficient Solvent content 2.14 42.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.994 α = 86.68 b = 46.005 β = 82.75 c = 71.762 γ = 68.48
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 PILATUS 2010-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.99 19.83 92.5 0.1 8.9 3.1 34329 2 21.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 2.09 67.8 0.32 4.3 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 3ADE 1.99 19.82 32617 1698 92.76 0.17195 0.1693 0.1749 0.22155 0.2217 RANDOM 10.168
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.92 r_dihedral_angle_4_deg 13.064 r_dihedral_angle_3_deg 11.835 r_dihedral_angle_1_deg 7.377 r_scangle_it 2.953 r_scbond_it 1.924 r_angle_other_deg 1.687 r_angle_refined_deg 1.587 r_mcangle_it 1.095 r_mcbond_it 0.553
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.92 r_dihedral_angle_4_deg 13.064 r_dihedral_angle_3_deg 11.835 r_dihedral_angle_1_deg 7.377 r_scangle_it 2.953 r_scbond_it 1.924 r_angle_other_deg 1.687 r_angle_refined_deg 1.587 r_mcangle_it 1.095 r_mcbond_it 0.553 r_mcbond_other 0.122 r_chiral_restr 0.097 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4310 Nucleic Acid Atoms Solvent Atoms 537 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing