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Structure of a Saccharomyces cerevisiae Mps1 peptide bound to dwarf Ndc80 Complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CTS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.1 291 13% polyethylene glycol 8000,
1M sodium chloride
100 mM PIPES pH 6.1
Crystal Properties Matthews coefficient Solvent content 4.03 69.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.657 α = 90 b = 168.295 β = 90 c = 230.214 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 77.36 PIXEL DECTRIS PILATUS 6M 2023-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 2.0.1 1.0309 ALS 2.0.1
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 3.02 115.11 64.98 0.155 0.181 0.068 0.994 5.3 6.1 18187 67.66
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 3.02 3.398 0.853 0.181 0.637 0.683 1.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.02 115.11 1.35 18002 900 64.14 0.2399 0.2381 0.2351 0.2707 0.2671 89.22
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 4.2623 f_angle_d 0.3489 f_chiral_restr 0.033 f_plane_restr 0.0018 f_bond_d 0.0011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5724 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement xia2 data reduction Aimless data scaling PHASER phasing