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Structure of SPOP MATH domain in complex with a Geminin peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6F8G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 One microliter of the protein complex in 20 mM Tris-HCl, pH 7.6, 50 mM NaCl and 5 mM dithiothreitol was mixed with on microliter of 0.2 M ammonium citrate dibasic and 20% (W/V) PEG 3350
Crystal Properties Matthews coefficient Solvent content 4.89 74.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.06 α = 90 b = 103.06 β = 90 c = 131.81 γ = 90
Symmetry Space Group P 41 21 2
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 210r 2020-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9786 APS 19-BM
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 3.39 47.99 99.8 0.096 15.24 37 10264 77.87
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 3.39 3.52 1.27
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6F8G 3.4 47.99 1.4 10264 1026 99.89 0.213 0.2098 0.2086 0.2414 0.2418 89.27
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 1.8538 f_angle_d 0.4792 f_chiral_restr 0.0389 f_plane_restr 0.0029 f_bond_d 0.0019
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2297 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 10
Software Software Software Name Purpose PHENIX refinement HKL-3000 data collection HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing