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Crystal structure of HP1alpha chromoshadow domain in complex with KAP1 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3I3C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1 M Bis-Tris pH 5.8, 0.2 M MgCl2, 20% PEG3350, 30 mM glycyl-glycyl-glycine
Crystal Properties Matthews coefficient Solvent content 3.54 60.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.809 α = 90 b = 107.809 β = 90 c = 64.612 γ = 120
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 200K 2021-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.4 46.68 100 0.083 0.088 0.028 0.999 16.5 9.5 16886
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 100 0.519 0.564 0.22 0.937 6.4
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 2.4 37.87 15941 875 99.66 0.2356 0.2346 0.2428 0.2523 0.2611 RANDOM 49.319
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] -2.19 -1.1 -2.19 7.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.387 r_dihedral_angle_3_deg 16.092 r_long_range_B_refined 11.008 r_long_range_B_other 11.002 r_scangle_other 9.079 r_mcangle_it 7.382 r_mcangle_other 7.38 r_dihedral_angle_1_deg 6.679 r_scbond_it 6.284 r_scbond_other 6.282
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.387 r_dihedral_angle_3_deg 16.092 r_long_range_B_refined 11.008 r_long_range_B_other 11.002 r_scangle_other 9.079 r_mcangle_it 7.382 r_mcangle_other 7.38 r_dihedral_angle_1_deg 6.679 r_scbond_it 6.284 r_scbond_other 6.282 r_mcbond_it 5.146 r_mcbond_other 5.138 r_angle_refined_deg 1.838 r_angle_other_deg 0.59 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2136 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing