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Crystal structure of the N-terminal parallel dimeric coiled-coil region of the human kinetochore associated protein Spindly
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 300 Bis-Tris Propane pH 6.5; 19% PEG3350; 0.2M KSCN
Crystal Properties Matthews coefficient Solvent content 3.73 67.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.507 α = 90 b = 112.507 β = 90 c = 49.642 γ = 120
Symmetry Space Group P 32 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 6M 2018-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966000 ESRF MASSIF-1
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 48.72 99.3 0.079 0.05 0.999 10.8 5.4 9079
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 2.95 1.558 0.97 0.718 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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION SIRAS FREE R-VALUE 2.8 48.72 9068 432 99.191 0.251 0.2492 0.2478 0.2898 0.286 92.609
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] -3.132 -1.566 -3.132 10.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 47.421 r_dihedral_angle_3_deg 28.291 r_dihedral_angle_4_deg 24.672 r_lrange_it 18.02 r_lrange_other 18.018 r_scangle_it 14.16 r_scangle_other 14.154 r_scbond_it 8.894 r_scbond_other 8.889 r_mcangle_other 7.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 47.421 r_dihedral_angle_3_deg 28.291 r_dihedral_angle_4_deg 24.672 r_lrange_it 18.02 r_lrange_other 18.018 r_scangle_it 14.16 r_scangle_other 14.154 r_scbond_it 8.894 r_scbond_other 8.889 r_mcangle_other 7.73 r_mcangle_it 7.724 r_dihedral_angle_1_deg 5.471 r_mcbond_it 5.383 r_mcbond_other 5.334 r_angle_refined_deg 1.887 r_angle_other_deg 1.381 r_nbd_refined 0.396 r_symmetry_nbd_other 0.261 r_nbd_other 0.259 r_symmetry_nbd_refined 0.202 r_symmetry_xyhbond_nbd_refined 0.195 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.09 r_bond_refined_d 0.019 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1598 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling CRANK2 phasing