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Crystal Structure of PHF1 Tudor domain in complex with a peptidomimetic ligand UNC6641
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HCZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277.15 0.01 M ZnCl2, 0.1 M MES pH 6.0 and 20% PEG 6000
Crystal Properties Matthews coefficient Solvent content 1.96 37.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.394 α = 90.02 b = 45.345 β = 95.19 c = 64.442 γ = 90.07
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CMOS RDI CMOS_8M 2020-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.28 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.85 43.22 90.87 0.997 8.85 1.9 37960
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 1.85 1.92 0.3336
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 THROUGHOUT 4HCZ 1.85 43.22 1.75 37960 2052 90.81 0.2372 0.2327 0.2378 0.281 0.2895 19.9801
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3982 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 137
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction autoXDS data reduction PHASER phasing