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Structure of fission yeast Duf89 protein bound to Co2+ and PO4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7T7N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 A solution containing 0.24 mM Duf89-D252N protein, 5 mM CoCl2, 10 mM sodium pyrophosphate (pH 6.5), 18.2 mM Tris-HCl (pH 7.5), 136.2 mM NaCl, and 0.455 mM EDTA was preincubated on ice for 30 min. Aliquots were then mixed with equal volume of precipitant solution containing 0.01 M ZnSO4, 0.2 M MES (pH 6.5), and 25% (v/v) PEG-550 MME. Cryoprotectant: 100% paraffin oil
Crystal Properties Matthews coefficient Solvent content 2.67 53.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.109 α = 90 b = 91.163 β = 90 c = 106.813 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS EIGER2 XE 9M 2023-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9795 NSLS-II 19-ID
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 2.06 50 99.1 0.109 0.039 0.996 25.8 8 34041 30.12
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 2.06 2.1 99.6 1.138 0.425 0.618 2
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 2.06 28.42 0.1 31191 1829 91.71 0.1767 0.1736 0.1736 0.2271 0.2267 41.57
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 8.4711 f_angle_d 1.1804 f_chiral_restr 0.0645 f_bond_d 0.0128 f_plane_restr 0.0092
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3439 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 42
Software Software Software Name Purpose PHENIX refinement PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing