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KLHDC2 Kelch Domain with KLHDC2 c-terminal peptide bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6DO3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 11mM Tris pH 8.0, 8mM Hexamine cobalt, 260-450 mM NaCl, and 24-34% PEG4000
Crystal Properties Matthews coefficient Solvent content 1.98 38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.51 α = 90 b = 88.19 β = 104.49 c = 89.34 γ = 90
Symmetry Space Group P 1 21 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 EIGER2 X 9M 2020-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
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 1.418 19.8 91.1 0.062 0.997 10.4 3.4 86639
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 1.418 1.552 0.747 0.461 1.5
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 (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 1.418 19.8 86639 4449 68.7 0.2006 0.1992 0.2078 0.228 0.2142 RANDOM 28.99
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] -0.0345 -0.4264 0.8486 -0.8141
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.28 t_omega_torsion 4.44 t_angle_deg 0.96 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.28 t_omega_torsion 4.44 t_angle_deg 0.96 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5363 Nucleic Acid Atoms Solvent Atoms 594 Heterogen Atoms 30
Software Software Software Name Purpose BUSTER refinement autoPROC data reduction autoPROC data scaling PHASER phasing