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Crystal structure of the KAP1 tripartite motif in complex with the ZNF93 KRAB domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QAJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 11% (w/v) PEG 5000 MME
5% Tacsimate
0.1 M HEPES pH 7
Crystal Properties Matthews coefficient Solvent content 3.32 62.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 190.283 α = 90 b = 68.583 β = 114.05 c = 149.111 γ = 90
Symmetry Space Group C 1 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 EIGER2 XE 16M 2021-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.8 63.79 97.26 0.07466 0.05181 0.985 20.87 2.8 42537 60.12
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 97.29 0.5035 0.3428 0.702 2.86 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 6QAJ 2.8 63.79 1.35 42489 2224 97.28 0.2291 0.2267 0.2259 0.274 0.2727 Test (R-free) flag value: 0 68.52
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 f_dihedral_angle_d 5.4624 f_angle_d 1.5512 f_chiral_restr 0.0608 f_plane_restr 0.0197 f_bond_d 0.0128
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7889 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 8
Software Software Software Name Purpose xia2 data reduction PHENIX refinement DIALS data scaling Coot model building PHASER phasing