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Crystal structure of the Kelch domain in complex with 11 amino acid peptide (model of the ETGE loop)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZGK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 1.8 M sodium acetate pH 7.0, 0.1 M Bis-Tris propane pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.18 61.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.296 α = 90 b = 75.296 β = 90 c = 127.539 γ = 120
Symmetry Space Group P 31 2 1
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 2M 2019-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.0 ELETTRA 5.2R
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 2.45 65.208 99.5 0.11 40.66 18.1 11948
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 2.7 2.8 0.614
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1zgk 2.75 17 11310 560 99.49 0.185 0.181 0.2584 0.2328 69.133
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] -0.06 -0.03 -0.06 0.196
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.296 r_dihedral_angle_4_deg 19.114 r_dihedral_angle_3_deg 16.645 r_lrange_it 10.99 r_lrange_other 10.988 r_dihedral_angle_1_deg 8.742 r_scangle_it 8.655 r_scangle_other 8.647 r_mcangle_it 7.247 r_mcangle_other 7.246
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.296 r_dihedral_angle_4_deg 19.114 r_dihedral_angle_3_deg 16.645 r_lrange_it 10.99 r_lrange_other 10.988 r_dihedral_angle_1_deg 8.742 r_scangle_it 8.655 r_scangle_other 8.647 r_mcangle_it 7.247 r_mcangle_other 7.246 r_scbond_it 5.518 r_scbond_other 5.494 r_mcbond_it 4.891 r_mcbond_other 4.874 r_angle_refined_deg 1.499 r_angle_other_deg 1.212 r_symmetry_nbd_refined 0.243 r_symmetry_xyhbond_nbd_refined 0.215 r_nbd_refined 0.201 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.166 r_nbd_other 0.157 r_xyhbond_nbd_refined 0.129 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.052 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2302 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling AMoRE phasing