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Crystal structure of human Spindlin1 in complex with a histone H4K20(me3) peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NS2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 1.5 M (NH4)2SO4, 0.1 M Bis-Tris
Crystal Properties Matthews coefficient Solvent content 2.55 51.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.769 α = 90 b = 148.504 β = 90 c = 169.212 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2017-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.9791 SSRF BL17U1
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 3.3 84.61 99 0.13 29.2 9.9 17175
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 3.3 3.36 100 0.45 10.2 4.5
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 2NS2 3.3 84.61 16247 903 99.48 0.22387 0.21922 0.2307 0.3081 0.3142 RANDOM 64.962
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] 8.08 -2.27 -5.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.046 r_dihedral_angle_3_deg 19.086 r_dihedral_angle_4_deg 16.376 r_long_range_B_refined 10.048 r_long_range_B_other 10.048 r_dihedral_angle_1_deg 8.896 r_mcangle_it 6.901 r_mcangle_other 6.901 r_scangle_other 6.007 r_mcbond_it 4.057
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.046 r_dihedral_angle_3_deg 19.086 r_dihedral_angle_4_deg 16.376 r_long_range_B_refined 10.048 r_long_range_B_other 10.048 r_dihedral_angle_1_deg 8.896 r_mcangle_it 6.901 r_mcangle_other 6.901 r_scangle_other 6.007 r_mcbond_it 4.057 r_mcbond_other 4.057 r_scbond_it 3.444 r_scbond_other 3.444 r_angle_refined_deg 1.782 r_angle_other_deg 1.053 r_chiral_restr 0.094 r_bond_refined_d 0.015 r_bond_other_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 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 6351 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing